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- PDB-8wu7: Structure of a cis-Geranylfarnesyl Diphosphate Synthase from Stre... -

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Basic information

Entry
Database: PDB / ID: 8wu7
TitleStructure of a cis-Geranylfarnesyl Diphosphate Synthase from Streptomyces clavuligerus
ComponentsIsoprenyl transferase
KeywordsBIOSYNTHETIC PROTEIN / cis-prenyltransferase
Function / homology
Function and homology information


Z-farnesyl diphosphate synthase activity / polyprenyltransferase activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / magnesium ion binding / plasma membrane
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
Isoprenyl transferase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLi, F.R. / Wang, Q.L. / Pan, X.M. / Dong, L.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073746 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase.
Authors: Li, F.R. / Wang, Q. / Pan, X. / Xu, H.M. / Dong, L.B.
History
DepositionOct 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)32,4781
Polymers32,4781
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.590, 61.170, 84.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Isoprenyl transferase


Mass: 32477.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: uppS2 / Organ: bacteria / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D5SL65
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.63 Å3/Da / Density % sol: 27.3 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 18% (w/v) Polyethylene glycol 4000, 0.1 M MES monohydrate (pH 5.7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.09→84.37 Å / Num. obs: 13544 / % possible obs: 99.6 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Net I/σ(I): 51.2
Reflection shellResolution: 2.09→2.15 Å / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 38.1 / Num. unique obs: 1033 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.20.1-4487)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTV4.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→30.59 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 1349 10 %
Rwork0.187 --
obs0.1913 13487 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 0 202 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.477
X-RAY DIFFRACTIONf_dihedral_angle_d4.122241
X-RAY DIFFRACTIONf_chiral_restr0.039254
X-RAY DIFFRACTIONf_plane_restr0.004292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.160.23721310.18721185X-RAY DIFFRACTION99
2.16-2.250.26091350.19591206X-RAY DIFFRACTION99
2.25-2.350.23521330.18621193X-RAY DIFFRACTION99
2.35-2.480.25511320.18821191X-RAY DIFFRACTION100
2.48-2.630.22711340.18371205X-RAY DIFFRACTION100
2.63-2.840.26041350.19091220X-RAY DIFFRACTION100
2.84-3.120.23141340.19981208X-RAY DIFFRACTION100
3.12-3.570.2071370.18241227X-RAY DIFFRACTION99
3.57-4.50.21791370.16641234X-RAY DIFFRACTION99
4.5-30.590.21871410.20091269X-RAY DIFFRACTION96

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