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- PDB-4kpj: Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Muta... -

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Basic information

Entry
Database: PDB / ID: 4kpj
TitleCrystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / Isoprene biosynthesis / Lipid synthesis / steroid biosynthesis / dimethylallyl pyrophosphate / Isoprenoid Pathway / Cholesterol Synthesis / Bisphosphonates
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / 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
PAMIDRONATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBarnett, B.L. / Tsoumpra, M.K. / Muniz, J.R.C. / Walter, R.L.
CitationJournal: To be Published
Title: Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate
Authors: Tsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Pilka, E. / Kwaasi, A. / Kavanagh, K.L. / Evdokimov, A.G. / Walter, R.L. / Ebetino, F.H. / Oppermann, U. / Russell, R.G.G. / Dunford, J.E.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,73311
Polymers43,0531
Non-polymers68010
Water4,756264
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,46722
Polymers86,1062
Non-polymers1,36120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7370 Å2
ΔGint-53 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.310, 111.310, 66.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1227-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase / FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / ...FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 43052.887 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: Y204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: PET 11 Derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID / Pamidronic acid


Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H11NO7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NH4Cl, 20% PEG6000, 10% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→55.65 Å / Num. all: 31105 / Num. obs: 31105 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 28.94 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.95-2.068.31.012228121100
2.06-55.658.80.13910.4311051100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP6

3cp6


Resolution: 1.95→50.84 Å / Cor.coef. Fo:Fc: 0.9481 / Cor.coef. Fo:Fc free: 0.9159 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1568 5.05 %RANDOM
Rwork0.1719 ---
all0.174 31105 --
obs0.174 31053 99.97 %-
Displacement parametersBiso mean: 34.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.7031 Å20 Å20 Å2
2--3.7031 Å20 Å2
3----7.4061 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 1.95→50.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 40 264 2994
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012877HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.883908HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1356SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes416HARMONIC5
X-RAY DIFFRACTIONt_it2877HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_chiral_improper_torsion364SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3738SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.01 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2344 138 4.92 %
Rwork0.2227 2668 -
all0.2233 2806 -
obs--99.97 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.19881.8977-1.66211.8979-0.49240.5254-0.0869-0.0410.02730.09530.2143-0.01660.3024-0.3166-0.12730.1246-0.10890.0016-0.12520.0928-0.0463-30.0139-0.341426.8487
20.4389-0.9661.10590.6283-1.01974.3166-0.0423-0.1678-0.08940.3696-0.0301-0.01590.08480.20420.07230.01560.00190.0059-0.08770.0096-0.0641-25.611216.261432.7924
30-0.5496-0.61682.8771-0.03262.57740.01490.1348-0.05160.26-0.03280.0740.4170.03790.01790.1293-0.0509-0.0534-0.0941-0.02570.1338-25.4947-6.48117.0002
41.7462-1.41450.36472.872-0.51521.28490.012-0.0847-0.16820.25070.00270.03860.27690.0159-0.0147-0.0173-0.0213-0.0212-0.0794-0.01040.0031-25.31736.341319.1027
51.064-0.05660.84111.33670.81256.58240.0176-0.2644-0.01960.195-0.02020.34710.0244-0.25480.0026-0.0773-0.00150.049-0.0061-0.03490.0864-37.771120.566519.901
61.4026-1.3995-0.00763.96050.05241.1249-0.02250.0025-0.01520.4396-0.0023-0.16340.17610.12250.0249-0.0058-0.0062-0.0552-0.0349-0.0119-0.0058-17.860510.373122.8736
71.555-1.39021.32162.6816-1.23132.37070.02760.0645-0.09250.096-0.0081-0.07880.10940.1309-0.0194-0.0763-0.0208-0.0095-0.0436-0.04090.0135-18.834813.09688.3072
82.5124-1.06381.88521.6437-0.60422.73040.0230.4404-0.1285-0.19070.0799-0.2005-0.20070.2221-0.1029-0.06140.00310.00150.0136-0.08880.043-29.483417.6224-2.4949
90.5833-0.63760.12911.410.13290.95230.06910.1168-0.177-0.0506-0.00880.11040.13160.0045-0.0603-0.0639-0.0193-0.0289-0.0738-0.04760.0348-30.83847.10424.5758
102.2653-0.0476-0.6144.18082.34322.7640.15660.28030.1504-0.2814-0.050.2932-0.3461-0.1365-0.10670.00750.0683-0.05630.0008-0.00770.0073-43.532223.5678-8.0501
110.6024-0.6876-0.67292.71140.61980.942-0.02090.0631-0.105-0.17290.03090.38160.0301-0.2312-0.01-0.0453-0.0213-0.0829-0.046-0.04690.0461-41.70358.0208-4.7272
1200.93180.92171.854-2.80292.7720.0456-0.0363-0.08770.23350.05710.07190.1203-0.0871-0.10270.0315-0.0454-0.0152-0.0903-0.0789-0.0025-30.4391-6.77814.3881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|9 - 28}A9 - 28
2X-RAY DIFFRACTION2{A|29 - 52}A29 - 52
3X-RAY DIFFRACTION3{A|53 - 78}A53 - 78
4X-RAY DIFFRACTION4{A|79 - 106}A79 - 106
5X-RAY DIFFRACTION5{A|107 - 124}A107 - 124
6X-RAY DIFFRACTION6{A|125 - 152}A125 - 152
7X-RAY DIFFRACTION7{A|153 - 177}A153 - 177
8X-RAY DIFFRACTION8{A|178 - 206}A178 - 206
9X-RAY DIFFRACTION9{A|207 - 268}A207 - 268
10X-RAY DIFFRACTION10{A|269 - 294}A269 - 294
11X-RAY DIFFRACTION11{A|295 - 332}A295 - 332
12X-RAY DIFFRACTION12{A|333 - 350}A333 - 350

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