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- PDB-7wmy: Crystal structure of methylenetetrahydrofolate reductase MSMEG_66... -

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Basic information

Entry
Database: PDB / ID: 7wmy
TitleCrystal structure of methylenetetrahydrofolate reductase MSMEG_6649 from Mycobacterium smegmatis with 5-methyltetrahydrofolate
Componentsmethylenetetrahydrofolate reductase
KeywordsTRANSFERASE / methylenetetrahydrofolate reductase
Function / homology: / Mycobacterial methylenetetrahydrofolate reductase / nucleotide binding / Methylenetetrahydrofolate reductase
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.266 Å
AuthorsLin, W. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903526 China
CitationJournal: Biochem.J. / Year: 2023
Title: Structural and functional characterization of a mycobacterial methylenetetrahydrofolate reductase utilizing NADH as the exclusive cofactor.
Authors: Li, J. / Yang, M. / Li, W. / Lu, C. / Feng, D. / Shang, Z. / Wang, C. / Lin, W.
History
DepositionJan 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methylenetetrahydrofolate reductase


Theoretical massNumber of molelcules
Total (without water)32,9791
Polymers32,9791
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13760 Å2
Unit cell
Length a, b, c (Å)85.830, 85.830, 104.593
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein methylenetetrahydrofolate reductase


Mass: 32978.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6649 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R6S0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Sodium cacodylate, calcium acetate, glycerol, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.266→60.59 Å / Num. obs: 21092 / % possible obs: 99.3 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.036 / Rrim(I) all: 0.128 / Net I/σ(I): 17.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.27-2.3913.31.3324060630570.7460.3791.3852.5100
7.17-60.5911.50.03286127510.9990.010.03455.899.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.266→37.165 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 1052 5 %
Rwork0.2106 20002 -
obs0.212 21054 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.83 Å2 / Biso mean: 51.2314 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.266→37.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 0 64 2345
Biso mean---52.24 -
Num. residues----295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2663-2.36940.27451400.26352475100
2.3694-2.49430.30631150.25672487100
2.4943-2.65050.28111190.25392497100
2.6505-2.85510.28861360.249234595
2.8551-3.14230.27161360.23782494100
3.1423-3.59670.25111160.21382533100
3.5967-4.53020.1921550.17472521100
4.5302-37.1650.23131350.19532650100

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