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- PDB-6g32: Crystal structure of human geranylgeranyl diphosphate synthase mu... -

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Basic information

Entry
Database: PDB / ID: 6g32
TitleCrystal structure of human geranylgeranyl diphosphate synthase mutant D188Y
ComponentsGeranylgeranyl pyrophosphate synthase
KeywordsTRANSFERASE / geranylgeranyl diphosphate synthase / mevalonate pathway / prenyltransferase / GGPPS
Function / homology
Function and homology information


isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity ...isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / isoprenoid biosynthetic process / Activation of gene expression by SREBF (SREBP) / Z disc / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Geranylgeranyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.281 Å
AuthorsLisnyansky, M. / Kapelushnik, N. / Ben-Bassat, A. / Marom, M. / Loewenstein, A. / Khananshvili, D. / Giladi, M. / Haitin, Y.
Funding support Israel, 4items
OrganizationGrant numberCountry
Other governmentIsrael Science Foundation (ISF) grant 1721/16 Israel
Other governmentIsrael Science Foundation (ISF) grant 1775/12 Israel
Other governmentIsrael Cancer Research Foundation (ICRF) grant 01214 Israel
German Research FoundationI-2425-418.13/2016 Israel
CitationJournal: Mol. Pharmacol. / Year: 2018
Title: Reduced Activity of Geranylgeranyl Diphosphate Synthase Mutant Is Involved in Bisphosphonate-Induced Atypical Fractures.
Authors: Lisnyansky, M. / Kapelushnik, N. / Ben-Bassat, A. / Marom, M. / Loewenstein, A. / Khananshvili, D. / Giladi, M. / Haitin, Y.
History
DepositionMar 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
C: Geranylgeranyl pyrophosphate synthase
D: Geranylgeranyl pyrophosphate synthase
E: Geranylgeranyl pyrophosphate synthase
F: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,45912
Polymers212,9066
Non-polymers5536
Water181
1
C: Geranylgeranyl pyrophosphate synthase
D: Geranylgeranyl pyrophosphate synthase
E: Geranylgeranyl pyrophosphate synthase
F: Geranylgeranyl pyrophosphate synthase
hetero molecules

A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,45912
Polymers212,9066
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area15290 Å2
ΔGint-108 kcal/mol
Surface area69950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.540, 148.540, 268.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Geranylgeranyl pyrophosphate synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Farnesyltranstransferase / Geranylgeranyl diphosphate synthase / Geranyltranstransferase


Mass: 35484.367 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGPS1 / Variant: Asp188Tyr / Production host: Escherichia coli (E. coli)
References: UniProt: O95749, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 3.6M Sodium formate, 0.01% w/v aspartame, 0.01% w/v gly-gly-gly, 0.01% w/v pentaglycine, 0.01% w/v tyr-ala, 0.01% w/v tyr-phe, 0.0018M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 3.19→48.901 Å / Num. obs: 50043 / % possible obs: 98.4 % / Redundancy: 4.54 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 7.76
Reflection shellResolution: 3.19→3.206 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q80
Resolution: 3.281→48.901 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2575 1978 5.03 %
Rwork0.2059 --
obs0.2085 39361 84.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.281→48.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12962 0 36 1 12999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713306
X-RAY DIFFRACTIONf_angle_d0.89318179
X-RAY DIFFRACTIONf_dihedral_angle_d14.6357740
X-RAY DIFFRACTIONf_chiral_restr0.0472116
X-RAY DIFFRACTIONf_plane_restr0.0062326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2814-3.36350.329160.3476272X-RAY DIFFRACTION9
3.3635-3.45440.3637340.3045832X-RAY DIFFRACTION26
3.4544-3.5560.3367800.29621721X-RAY DIFFRACTION55
3.556-3.67080.34191760.29333046X-RAY DIFFRACTION99
3.6708-3.80190.32151570.24863135X-RAY DIFFRACTION100
3.8019-3.95410.29781640.23483128X-RAY DIFFRACTION100
3.9541-4.13390.26521720.21783123X-RAY DIFFRACTION100
4.1339-4.35180.24931720.20633135X-RAY DIFFRACTION100
4.3518-4.62420.23631750.18523125X-RAY DIFFRACTION100
4.6242-4.98090.23391570.17452952X-RAY DIFFRACTION93
4.9809-5.48160.25051590.19993090X-RAY DIFFRACTION97
5.4816-6.27340.32951780.24163184X-RAY DIFFRACTION100
6.2734-7.89840.26171690.2113247X-RAY DIFFRACTION100
7.8984-48.90670.18811690.1573393X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.1508-1.0950.53377.7670.7026.5269-0.23160.0019-1.04720.4542-0.04971.32260.1066-1.02880.88840.4696-0.10850.14250.8109-0.030.536840.414410.871624.1929
21.1913-2.7949-2.25116.84135.31534.16730.2369-0.2378-0.6940.6275-0.68581.16290.4511-0.28570.43250.77990.1406-0.17091.0693-0.15720.803434.92232.357436.0645
30.49130.5673-0.54083.57570.70810.9795-0.0672-0.35330.24750.3898-0.01040.1752-0.1776-0.13050.11870.53980.1408-0.05350.7282-0.05760.399147.946427.858727.7304
44.6743-3.6750.58084.47810.56340.65260.06010.0894-0.47490.68360.21970.00390.4842-0.2166-0.40170.73460.0167-0.12670.5566-0.02970.557954.020129.506743.13
56.0083-1.01241.12788.7449-2.2446.9326-0.1319-0.3402-0.05540.72020.2871-1.22520.67061.3981-0.29140.56720.0813-0.04420.7734-0.10240.458368.551426.920148.1319
68.6357-2.57930.54582.04510.18982.503-0.563-1.2385-0.4420.45850.45070.3598-0.4486-0.19830.22570.77060.1911-0.04080.5827-0.0110.575445.855839.647247.7995
76.0895-1.44293.18920.3928-0.4257.40910.10960.20870.0549-0.4046-0.0455-0.0080.15220.2683-0.00740.65160.0164-0.0980.51860.01780.393360.353722.74267.954
80.98321.23530.02963.16231.63161.35690.12540.2223-0.0602-0.25770.0204-0.0388-0.108-0.2426-0.12880.46980.02660.0250.5190.020.37650.181212.85296.8668
91.4168-2.35662.56627.6362-5.24069.55290.06010.1787-0.1513-0.39780.01980.01850.71970.1122-0.11530.3047-0.0230.03740.4788-0.11850.383756.8447-1.586-0.4606
102.175-1.77370.9948.8085-3.28533.0094-0.06620.6590.5564-0.5113-0.4794-0.5491-0.680.88520.56370.8864-0.07550.07830.70820.10560.61485.211441.8501-38.1013
115.1707-1.35130.40610.7651-0.94341.3089-0.08530.55790.2220.0573-0.0194-0.0094-0.29190.25510.12160.7505-0.02920.04520.6454-0.00470.425473.888335.6744-35.4879
122.97692.07352.7832.16090.51934.3720.1030.10440.4811-0.12130.1023-0.365-0.93060.8408-0.21560.7621-0.04530.12790.5846-0.09840.567569.591842.3107-45.6476
133.53861.46321.58218.9761.26442.4061-0.08860.49550.1881-1.1392-0.0773-0.1221-0.14210.17070.09790.63760.07520.15130.5884-0.00520.425863.322535.2393-55.6999
141.58761.45341.6513.28253.10984.16710.1787-0.24130.03590.3058-0.0586-0.0803-0.1554-0.4862-0.1240.7293-0.03590.10910.6268-0.02060.5768.8626.0623-15.6579
153.02471.1147-0.13541.49250.6450.3166-0.2493-0.41130.20020.46920.2026-0.034-0.41240.2086-0.00140.86910.06410.02050.5412-0.04350.434181.171831.7656-16.2941
161.3232-1.8146-1.89235.57470.80595.010.28860.1741-0.2733-0.7272-0.5880.8291-0.2281-0.9580.2820.3993-0.093-0.10540.6240.01080.473786.490414.3491-11.0974
171.2914-1.38980.97597.22724.80167.05720.11910.05380.06550.63540.0997-0.27380.99650.2026-0.19920.4747-0.1414-0.02390.5404-0.02230.403688.065411.1548-7.2706
184.32291.339-0.42734.3055-0.69010.1160.1080.1494-0.1891.02150.2393-0.8814-0.4149-0.4191-0.14820.78440.1554-0.14441.0147-0.16120.6659106.2678-3.7007-24.4291
190.6582-0.68180.88497.35351.20061.8094-0.6441-1.1725-1.18660.61422.05510.342-0.419-0.8169-0.83580.67530.20250.061.41290.05491.2729108.8688-27.4281-16.3979
203.4879-0.33-0.17451.53070.49521.98750.5039-0.371-1.3984-0.17580.2411-0.79710.47530.4865-0.71230.53970.1449-0.13710.8493-0.06620.8703106.7217-17.92-24.9191
213.5371-1.8558-0.88451.9634-0.10162.49680.1433-0.1736-0.2880.12370.1449-0.58410.51880.2448-0.41670.49990.0773-0.14970.9418-0.04670.7522103.1338-11.2547-28.8418
221.93431.5845-2.54733.6026-1.12764.2046-0.0995-0.399-0.15140.00990.2176-0.63230.38160.18360.02430.57410.1001-0.05220.8215-0.15930.7242103.1124-28.638-33.7071
235.7341-1.1878-0.04731.5229-1.48231.78410.1982-0.36580.23880.30640.4024-0.42420.34980.2881-0.34990.75650.181-0.10420.7141-0.21290.830588.1917-30.434-26.924
249.45870.68241.3112.04770.01384.7048-0.1477-0.2811-0.68940.01970.29210.69940.21540.6074-0.16010.54760.2096-0.00290.663-0.00520.680574.14-27.4246-31.2396
256.7576-2.82044.0424.87830.22626.5539-0.8963-2.2695-2.77550.18081.2043-0.2894-0.1875-0.547-0.32510.61430.0669-0.11580.73010.05211.257293.2039-41.6621-21.4166
266.79090.1117-0.66264.33510.90211.8365-1.6006-1.5883-0.51090.82661.69150.69040.7052-0.2089-0.26191.37480.3663-0.10721.01590.18470.91699.927-36.7521-13.588
272.8435-0.299-1.21274.4158-1.32351.1354-0.27880.459-1.2189-1.02450.15070.08440.10890.1239-0.26060.7741-0.1213-0.02810.9346-0.05780.860599.3046-20.7619-50.2485
283.97062.99651.85442.2261.38490.8626-0.4098-0.1541-0.1276-0.59770.4494-0.8267-0.3366-0.354-0.21650.99870.30250.23761.3840.33391.2637118.1922-5.7967-57.7456
295.7889-2.22950.86840.8389-0.18160.8672-0.110.1755-0.1526-0.3850.4112-0.9106-0.03440.8413-0.09670.53110.13270.13030.9552-0.23270.9127105.0676-12.1933-46.9763
301.22240.7110.99763.2082-1.82452.84350.09490.5422-0.0429-0.4174-0.0049-0.66030.24530.2724-0.06880.5971-0.00910.14250.9013-0.14240.8042114.28431.3457-43.2557
310.54860.04211.1243.1212-0.44542.3735-0.71580.4566-0.1803-1.51550.19430.45440.5760.5818-0.48560.7037-0.13070.05561.15860.01331.020196.27989.2934-47.5785
329.3516-2.9620.54576.96144.7214.30860.0316-0.26990.941-0.17890.1172-0.6869-0.19370.3746-0.28440.5455-0.05610.15130.92640.11980.724496.608719.1239-43.0459
337.4869-2.8584-0.57641.91271.32511.73170.33372.01561.0865-0.4659-0.1228-0.9244-0.23520.3064-0.16840.8665-0.10370.37911.22660.08251.1628117.914811.8963-56.2146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 214 )
5X-RAY DIFFRACTION5chain 'A' and (resid 215 through 255 )
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 296 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 223 )
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 296 )
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 42 )
11X-RAY DIFFRACTION11chain 'C' and (resid 43 through 152 )
12X-RAY DIFFRACTION12chain 'C' and (resid 153 through 214 )
13X-RAY DIFFRACTION13chain 'C' and (resid 215 through 296 )
14X-RAY DIFFRACTION14chain 'D' and (resid 6 through 84 )
15X-RAY DIFFRACTION15chain 'D' and (resid 85 through 173 )
16X-RAY DIFFRACTION16chain 'D' and (resid 174 through 223 )
17X-RAY DIFFRACTION17chain 'D' and (resid 224 through 296 )
18X-RAY DIFFRACTION18chain 'E' and (resid 5 through 20 )
19X-RAY DIFFRACTION19chain 'E' and (resid 21 through 42 )
20X-RAY DIFFRACTION20chain 'E' and (resid 43 through 67 )
21X-RAY DIFFRACTION21chain 'E' and (resid 68 through 108 )
22X-RAY DIFFRACTION22chain 'E' and (resid 109 through 173 )
23X-RAY DIFFRACTION23chain 'E' and (resid 174 through 223 )
24X-RAY DIFFRACTION24chain 'E' and (resid 224 through 255 )
25X-RAY DIFFRACTION25chain 'E' and (resid 256 through 277 )
26X-RAY DIFFRACTION26chain 'E' and (resid 278 through 295 )
27X-RAY DIFFRACTION27chain 'F' and (resid 5 through 20 )
28X-RAY DIFFRACTION28chain 'F' and (resid 21 through 42 )
29X-RAY DIFFRACTION29chain 'F' and (resid 43 through 108 )
30X-RAY DIFFRACTION30chain 'F' and (resid 109 through 194 )
31X-RAY DIFFRACTION31chain 'F' and (resid 195 through 214 )
32X-RAY DIFFRACTION32chain 'F' and (resid 215 through 255 )
33X-RAY DIFFRACTION33chain 'F' and (resid 256 through 295 )

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