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- PDB-6kd7: Crystal structure of geranylgeranyl pyrophosphate synthase -

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Basic information

Entry
Database: PDB / ID: 6kd7
TitleCrystal structure of geranylgeranyl pyrophosphate synthase
ComponentsPolyprenyl synthetase
KeywordsTRANSFERASE / prenyltransferase
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process
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
PYROPHOSPHATE / Polyprenyl synthetase
Similarity search - Component
Biological speciesNonlabens dokdonensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKim, S. / Kim, K.-J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6.
Authors: Kim, S. / Kim, E.J. / Park, J.B. / Kim, S.W. / Kim, K.J.
History
DepositionJul 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Polyprenyl synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5866
Polymers38,1751
Non-polymers4115
Water3,387188
1
A: Polyprenyl synthetase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)231,51636
Polymers229,0526
Non-polymers2,46530
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area22500 Å2
ΔGint-238 kcal/mol
Surface area79080 Å2
MethodPISA
2
A: Polyprenyl synthetase
hetero molecules

A: Polyprenyl synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,17212
Polymers76,3512
Non-polymers82210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Buried area5890 Å2
ΔGint-72 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.718, 194.718, 107.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Polyprenyl synthetase


Mass: 38175.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nonlabens dokdonensis (strain DSM 17205 / KCTC 12402 / DSW-6) (bacteria)
Gene: DDD_1788 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7W5I6
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 7.96 Å3/Da / Density % sol: 84.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Ammonium sulfate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 78959 / % possible obs: 97.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 28.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3761 / % possible all: 94.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JFQ

5jfq


Resolution: 2→36.43 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.267 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 3920 5 %RANDOM
Rwork0.2223 ---
obs0.227 75037 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.49 Å2 / Biso mean: 37.059 Å2 / Biso min: 17.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å2-0 Å2
2---0.08 Å20 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 2→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 23 188 2812
Biso mean--74.88 42.79 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132734
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172506
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.6413693
X-RAY DIFFRACTIONr_angle_other_deg1.5041.5835838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55824.46139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01115503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9881510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022989
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02529
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 254 -
Rwork0.427 5328 -
all-5582 -
obs--94.87 %

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