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- PDB-8hdl: Crystal structure of ASFV trans geranylgeranyl diphosphate syntha... -

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Basic information

Entry
Database: PDB / ID: 8hdl
TitleCrystal structure of ASFV trans geranylgeranyl diphosphate synthase B318L
ComponentsTrans-prenyltransferase
KeywordsTRANSFERASE / ASFV
Function / homology
Function and homology information


geranylfarnesyl diphosphate synthase activity / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / farnesyltranstransferase activity ...geranylfarnesyl diphosphate synthase activity / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / farnesyltranstransferase activity / geranyltranstransferase activity / host cell endoplasmic reticulum / host cell membrane / membrane / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 2. / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Trans-prenyltransferase
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.198 Å
AuthorsZhao, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Exploring AlphaFold2's Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein.
Authors: Zhao, H. / Zhang, H. / She, Z. / Gao, Z. / Wang, Q. / Geng, Z. / Dong, Y.
History
DepositionNov 4, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trans-prenyltransferase


Theoretical massNumber of molelcules
Total (without water)32,3291
Polymers32,3291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.130, 56.130, 376.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Trans-prenyltransferase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate ...(2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Farnesyltranstransferase / Geranyltranstransferase / Polyprenyl-diphosphate synthase


Mass: 32329.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted)
Gene: Ba71V-074, B318L / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q65164, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.198→48.21 Å / Num. obs: 6579 / % possible obs: 99.7 % / Redundancy: 31.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.297 / Net I/σ(I): 15.6
Reflection shellResolution: 3.2→3.28 Å / Num. unique obs: 472 / CC1/2: 0.718

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 3.198→48.21 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2838 658 10 %
Rwork0.2458 --
obs0.2497 6578 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.198→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 0 0 2058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082108
X-RAY DIFFRACTIONf_angle_d1.4212848
X-RAY DIFFRACTIONf_dihedral_angle_d26.467761
X-RAY DIFFRACTIONf_chiral_restr0.068312
X-RAY DIFFRACTIONf_plane_restr0.011364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1982-3.44510.38051250.32161133X-RAY DIFFRACTION100
3.4451-3.79160.33081260.27761133X-RAY DIFFRACTION100
3.7916-4.340.26031300.23961159X-RAY DIFFRACTION100
4.34-5.46670.27651310.23421190X-RAY DIFFRACTION100
5.4667-48.210.26881460.23361305X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.0849 Å / Origin y: 14.7343 Å / Origin z: -14.278 Å
111213212223313233
T0.6118 Å2-0.0378 Å2-0.0014 Å2-0.7406 Å2-0.1615 Å2--0.7292 Å2
L1.3257 °20.0158 °2-0.4477 °2-1.5572 °2-0.104 °2--2.2252 °2
S-0.0628 Å °-0.3016 Å °0.136 Å °-0.1575 Å °0.0296 Å °0.0399 Å °0.1149 Å °-0.2272 Å °0.0357 Å °
Refinement TLS groupSelection details: all

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