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- PDB-8zsa: Crystal structure of 4VPMT2 -

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Basic information

Entry
Database: PDB / ID: 8zsa
TitleCrystal structure of 4VPMT2
Components4VPMT2
KeywordsTRANSFERASE / methyltransferase / 4-vinylanisole biosynthesis
Function / homology4-ethenylphenol / S-ADENOSYLMETHIONINE
Function and homology information
Biological speciesLocusta migratoria (migratory locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsGao, L. / Yang, J. / Lei, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22193073 and 92253305 China
CitationJournal: To Be Published
Title: Crystal structure of 4VPMT2
Authors: Gao, L. / Yang, J. / Lei, X.G.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4VPMT2
B: 4VPMT2
C: 4VPMT2
D: 4VPMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5389
Polymers147,8254
Non-polymers1,7145
Water64936
1
A: 4VPMT2
C: 4VPMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8295
Polymers73,9122
Non-polymers9173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-16 kcal/mol
Surface area22410 Å2
MethodPISA
2
B: 4VPMT2
D: 4VPMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7094
Polymers73,9122
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-13 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.525, 101.525, 326.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
4VPMT2


Mass: 36956.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Locusta migratoria (migratory locust) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4VP / 4-ethenylphenol


Mass: 120.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 MMT buffer, 25% PEG1500, pH7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 38865 / % possible obs: 98.8 % / Redundancy: 11.9 % / CC1/2: 0.955 / Rrim(I) all: 0.36 / Net I/σ(I): 10.5
Reflection shellResolution: 3.4→3.46 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1303 / CC1/2: 0.629 / % possible all: 87.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→29.62 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 3144 8.09 %
Rwork0.2124 --
obs0.2152 38865 76.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.42→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8811 0 117 36 8964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029168
X-RAY DIFFRACTIONf_angle_d0.5212498
X-RAY DIFFRACTIONf_dihedral_angle_d5.8531231
X-RAY DIFFRACTIONf_chiral_restr0.0411393
X-RAY DIFFRACTIONf_plane_restr0.0051608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.470.3115450.3069523X-RAY DIFFRACTION25
3.47-3.530.3777700.3309753X-RAY DIFFRACTION35
3.53-3.590.3217850.2909967X-RAY DIFFRACTION46
3.59-3.650.3928970.31131083X-RAY DIFFRACTION52
3.65-3.720.3151050.29781144X-RAY DIFFRACTION53
3.72-3.80.29581080.27461171X-RAY DIFFRACTION56
3.8-3.880.30851040.26251231X-RAY DIFFRACTION57
3.88-3.970.30881130.24711276X-RAY DIFFRACTION61
3.97-4.070.28781310.22151478X-RAY DIFFRACTION67
4.07-4.180.22691330.21241546X-RAY DIFFRACTION73
4.18-4.30.25581350.20961651X-RAY DIFFRACTION78
4.3-4.440.21671640.19571878X-RAY DIFFRACTION87
4.44-4.60.23381830.19672000X-RAY DIFFRACTION93
4.6-4.780.20631720.20342006X-RAY DIFFRACTION96
4.78-50.21311950.20562116X-RAY DIFFRACTION99
5-5.260.31661860.21522129X-RAY DIFFRACTION100
5.26-5.590.23271870.2132149X-RAY DIFFRACTION100
5.59-6.020.27971980.2282103X-RAY DIFFRACTION100
6.02-6.610.26291960.22322134X-RAY DIFFRACTION100
6.62-7.550.21411820.19912115X-RAY DIFFRACTION100
7.56-9.470.20231760.15862143X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.3352 Å / Origin y: 2.0404 Å / Origin z: 8.2938 Å
111213212223313233
T0.4775 Å20.1134 Å20.0823 Å2-0.2977 Å2-0.0104 Å2--0.2852 Å2
L0.6833 °2-0.086 °2-0.1107 °2-0.8657 °2-0.2704 °2--1.0009 °2
S-0.1339 Å °0.1324 Å °-0.0447 Å °0.0455 Å °-0.1826 Å °-0.059 Å °0.1747 Å °-0.1083 Å °0.2274 Å °
Refinement TLS groupSelection details: all

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