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- PDB-7my6: Se-CrtE C-term His-tag with IPP added -

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Basic information

Entry
Database: PDB / ID: 7my6
TitleSe-CrtE C-term His-tag with IPP added
ComponentsFarnesyl-diphosphate synthase
KeywordsTRANSFERASE / Prenyl transferase / Isopentenyl pyrophosphate / Dimethylallyl pyrophosphate / cyanobacteria / terpenoids
Function / homology
Function and homology information


(2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / isoprenoid biosynthetic process
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Farnesyl-diphosphate synthase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPeat, T.S. / Newman, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2022
Title: Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase.
Authors: Satta, A. / Esquirol, L. / Ebert, B.E. / Newman, J. / Peat, T.S. / Plan, M. / Schenk, G. / Vickers, C.E.
History
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyl-diphosphate synthase
B: Farnesyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33318
Polymers67,1852
Non-polymers1,14816
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-160 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.423, 144.627, 48.066
Angle α, β, γ (deg.)90.000, 95.249, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Farnesyl-diphosphate synthase


Mass: 33592.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: Synpcc7942_0776 / Production host: Escherichia coli (E. coli)
References: UniProt: Q31Q61, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 7 types, 264 molecules

#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 200 nL of protein at 10 mg/mL was added to 200 nL of reservoir consisting of 90 mM CHES pH 9.5, 180 mM magnesium sulfate, 100 mM trisodium citrate, 22.5% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.94→48.21 Å / Num. obs: 45579 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.986 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.113 / Net I/σ(I): 5.7
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 9.7 % / Rmerge(I) obs: 2.327 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3076 / CC1/2: 0.392 / Rpim(I) all: 0.781

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7mxz

7mxz


Resolution: 2.02→45.482 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.163 / SU B: 5.122 / SU ML: 0.134 / Average fsc free: 0.9021 / Average fsc work: 0.9103 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2088 2053 5.092 %
Rwork0.1804 38268 -
all0.182 --
obs-40321 99.866 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.512 Å2-0 Å2-0.154 Å2
2---1.333 Å2-0 Å2
3---1.842 Å2
Refinement stepCycle: LAST / Resolution: 2.02→45.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 63 248 4658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154376
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6356115
X-RAY DIFFRACTIONr_angle_other_deg1.3931.57510058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1615577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02821.786224
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.13101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32515749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.681534
X-RAY DIFFRACTIONr_chiral_restr0.0720.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
X-RAY DIFFRACTIONr_nbd_refined0.2170.21130
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24081
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22272
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2249
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0920.210
X-RAY DIFFRACTIONr_nbd_other0.1530.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.215
X-RAY DIFFRACTIONr_mcbond_it1.6622.1842308
X-RAY DIFFRACTIONr_mcbond_other1.6622.1822307
X-RAY DIFFRACTIONr_mcangle_it2.6393.2572885
X-RAY DIFFRACTIONr_mcangle_other2.6393.2582886
X-RAY DIFFRACTIONr_scbond_it2.622.5562195
X-RAY DIFFRACTIONr_scbond_other2.592.5392180
X-RAY DIFFRACTIONr_scangle_it4.1223.6943230
X-RAY DIFFRACTIONr_scangle_other4.1053.6663207
X-RAY DIFFRACTIONr_lrange_it6.73841.14319679
X-RAY DIFFRACTIONr_lrange_other6.68541.09819506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.0720.2771590.2782803X-RAY DIFFRACTION100
2.072-2.1290.2931340.2382755X-RAY DIFFRACTION99.9308
2.129-2.1910.2251450.232699X-RAY DIFFRACTION99.9649
2.191-2.2580.2211330.2162588X-RAY DIFFRACTION99.9633
2.258-2.3320.2331510.1992487X-RAY DIFFRACTION100
2.332-2.4130.2331350.192456X-RAY DIFFRACTION99.9229
2.413-2.5040.1991270.182352X-RAY DIFFRACTION100
2.504-2.6060.2511180.1772220X-RAY DIFFRACTION99.9572
2.606-2.7220.1951360.1742193X-RAY DIFFRACTION100
2.722-2.8540.2371240.1762079X-RAY DIFFRACTION99.9546
2.854-3.0080.2151070.1661987X-RAY DIFFRACTION99.9523
3.008-3.1890.199800.1641852X-RAY DIFFRACTION99.3316
3.189-3.4080.195640.1681787X-RAY DIFFRACTION100
3.408-3.680.188700.1641666X-RAY DIFFRACTION99.9424
3.68-4.0280.212820.1551512X-RAY DIFFRACTION99.9373
4.028-4.4990.15870.1481357X-RAY DIFFRACTION100
4.499-5.1870.171770.1481192X-RAY DIFFRACTION99.9213
5.187-6.3320.208570.2121030X-RAY DIFFRACTION99.9081
6.332-8.8690.173510.146783X-RAY DIFFRACTION99.2857
8.869-45.4820.162160.163470X-RAY DIFFRACTION98.5801

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