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

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Basic information

Entry
Database: PDB / ID: 8ylz
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 / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] 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: 1.6 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
DepositionMar 7, 2024Deposition 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
Water3,711206
1
A: Isoprenyl transferase

A: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)64,9552
Polymers64,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2970 Å2
ΔGint-8 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.580, 61.140, 84.340
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.: 206 / 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: 1.73 Å3/Da / Density % sol: 28.8 %
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: 1.6→34.94 Å / Num. obs: 27160 / % possible obs: 91.3 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.015 / Rrim(I) all: 0.048 / Χ2: 0.89 / Net I/σ(I): 33.2 / Num. measured all: 298879
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 94.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.127 / Num. measured all: 12444 / Num. unique obs: 1362 / CC1/2: 0.989 / Rpim(I) all: 0.044 / Rrim(I) all: 0.135 / Χ2: 0.52 / Net I/σ(I) obs: 11.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
pointlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30.57 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1999 7.38 %RANDOM
Rwork0.1945 ---
obs0.1969 27098 90.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 0 206 1822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.917
X-RAY DIFFRACTIONf_dihedral_angle_d5.399241
X-RAY DIFFRACTIONf_chiral_restr0.06254
X-RAY DIFFRACTIONf_plane_restr0.014292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.21831460.16881829X-RAY DIFFRACTION94
1.64-1.680.22671530.18211924X-RAY DIFFRACTION100
1.68-1.730.27061520.19311922X-RAY DIFFRACTION99
1.73-1.790.25021550.19261921X-RAY DIFFRACTION99
1.79-1.850.23931530.18131927X-RAY DIFFRACTION99
1.85-1.920.2583980.21241225X-RAY DIFFRACTION75
1.93-2.020.23481130.1911424X-RAY DIFFRACTION79
2.02-2.120.22411300.19921642X-RAY DIFFRACTION84
2.12-2.250.1991480.18531855X-RAY DIFFRACTION99
2.27-2.430.1961410.19091762X-RAY DIFFRACTION100
2.43-2.670.23111560.19851957X-RAY DIFFRACTION100
2.69-3.060.24061500.20681885X-RAY DIFFRACTION100
3.06-3.850.21521460.18311831X-RAY DIFFRACTION91
3.85-30.570.22721580.20561995X-RAY DIFFRACTION94

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