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- PDB-8z9u: Crystal structure of the Methermicoccus shengliensis ZC-1 2-metho... -

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Basic information

Entry
Database: PDB / ID: 8z9u
TitleCrystal structure of the Methermicoccus shengliensis ZC-1 2-methoxybenzoic acid methyltransferase (MtxA)
ComponentsTetrahydromethanopterin S-methyltransferase subunit H
KeywordsTRANSFERASE / Homodimers / Methyltransferase
Function / homologyTetrahydromethanopterin S-methyltransferase subunit H / tetrahydromethanopterin S-methyltransferase / Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / Dihydropteroate synthase-like / one-carbon metabolic process / methyltransferase activity / methylation / Tetrahydromethanopterin S-methyltransferase subunit H
Function and homology information
Biological speciesMethermicoccus shengliensis DSM 18856 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsYang, Q. / Wang, S.X. / Bai, L.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of the Methermicoccus shengliensis ZC-1 2-methoxybenzoic acid methyltransferase (MtxA)
Authors: Yang, Q. / Wang, S.X. / Bai, L.P.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Tetrahydromethanopterin S-methyltransferase subunit H
A: Tetrahydromethanopterin S-methyltransferase subunit H


Theoretical massNumber of molelcules
Total (without water)75,7482
Polymers75,7482
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-44 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.716, 83.214, 132.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tetrahydromethanopterin S-methyltransferase subunit H


Mass: 37873.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Methermicoccus shengliensis DSM 18856 is not available, replaced by A0A832VZ83 temporarily.
Source: (gene. exp.) Methermicoccus shengliensis DSM 18856 (archaea)
Gene: mtrH, HA299_01740 / Production host: Methanococcus maripaludis S2 (archaea)
References: UniProt: A0A832VZ83, tetrahydromethanopterin S-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5 42% % v/v Polyethylene glycol 200 pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.91→50.51 Å / Num. obs: 67410 / % possible obs: 95.28 % / Redundancy: 11.9 % / Biso Wilson estimate: 29.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 15.3
Reflection shellResolution: 1.91→2.051 Å / Num. unique obs: 58060 / CC1/2: 0.779 / CC star: 0.998

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Processing

Software
NameVersionClassification
PHENIXv1.20.1_4487refinement
HKL-2000data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→39.01 Å / SU ML: 0.2167 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.8035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 3491 5.18 %
Rwork0.2124 63919 -
obs0.2134 67410 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.66 Å2
Refinement stepCycle: LAST / Resolution: 1.91→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 0 291 4628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744415
X-RAY DIFFRACTIONf_angle_d0.96015956
X-RAY DIFFRACTIONf_chiral_restr0.0588678
X-RAY DIFFRACTIONf_plane_restr0.0063763
X-RAY DIFFRACTIONf_dihedral_angle_d6.0112590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.31071300.28042529X-RAY DIFFRACTION99.18
1.93-1.960.28121330.26442504X-RAY DIFFRACTION100
1.96-1.990.26781270.25392539X-RAY DIFFRACTION100
1.99-2.020.26241480.23062530X-RAY DIFFRACTION100
2.02-2.060.24471180.22212525X-RAY DIFFRACTION99.96
2.06-2.090.24591380.21522534X-RAY DIFFRACTION100
2.09-2.130.24231400.20772528X-RAY DIFFRACTION100
2.13-2.170.23911450.20662514X-RAY DIFFRACTION100
2.17-2.210.23881460.20782535X-RAY DIFFRACTION100
2.21-2.260.241620.20942500X-RAY DIFFRACTION100
2.26-2.320.2611470.2112540X-RAY DIFFRACTION100
2.32-2.370.23891490.21352552X-RAY DIFFRACTION100
2.37-2.440.25341440.21672516X-RAY DIFFRACTION99.96
2.44-2.510.22961270.20632559X-RAY DIFFRACTION100
2.51-2.590.23361270.22082566X-RAY DIFFRACTION100
2.59-2.680.28291340.22092546X-RAY DIFFRACTION100
2.68-2.790.25391530.2322537X-RAY DIFFRACTION100
2.79-2.920.2241370.22592565X-RAY DIFFRACTION99.96
2.92-3.070.25011240.23222578X-RAY DIFFRACTION100
3.07-3.260.25861330.22422569X-RAY DIFFRACTION100
3.26-3.520.2181420.21362578X-RAY DIFFRACTION100
3.52-3.870.22851330.19552598X-RAY DIFFRACTION99.96
3.87-4.430.22921460.19342606X-RAY DIFFRACTION100
4.43-5.570.19491480.1942641X-RAY DIFFRACTION99.96
5.58-39.010.20031600.20732730X-RAY DIFFRACTION99.35

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