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

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Basic information

Entry
Database: PDB / ID: 7wmw
TitleCrystal structure of methylenetetrahydrofolate reductase MSMEG_6649 from Mycobacterium smegmatis
ComponentsMethylenetetrahydrofolate reductase
KeywordsTRANSFERASE / methylenetetrahydrofolate reductase
Function / homology: / Mycobacterial methylenetetrahydrofolate reductase / TIM Barrel - #220 / nucleotide binding / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Methylenetetrahydrofolate reductase
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.053 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
Water73941
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 area12560 Å2
Unit cell
Length a, b, c (Å)67.815, 67.815, 130.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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.: 41 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, Bis-Tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 36223 / % possible obs: 99.79 % / Redundancy: 16 % / CC1/2: 0.972 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.47
Reflection shellResolution: 2.05→2.07 Å / Num. unique obs: 36223 / CC1/2: 0.871

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.053→32.601 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 3625 10.01 %
Rwork0.2338 32598 -
obs0.2363 36223 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.96 Å2 / Biso mean: 56.4975 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.053→32.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 0 41 2165
Biso mean---56.9 -
Num. residues----271
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.053-2.07960.4021340.4301121798
2.0796-2.10810.42411390.41461255100
2.1081-2.13820.39061440.3881253100
2.1382-2.17010.38511380.37671242100
2.1701-2.2040.36721390.34511262100
2.204-2.24010.40831370.34581254100
2.2401-2.27870.36771410.36771260100
2.2787-2.32020.37381360.31771242100
2.3202-2.36480.38751420.33311249100
2.3648-2.4130.3021450.29521296100
2.413-2.46550.27981410.27451229100
2.4655-2.52280.37191400.29141268100
2.5228-2.58590.38151380.30351247100
2.5859-2.65580.36421390.29731259100
2.6558-2.73390.34461420.29881244100
2.7339-2.82210.31241370.29671273100
2.8221-2.92290.31741390.31481236100
2.9229-3.03980.34551350.29771250100
3.0398-3.17810.32531430.28181272100
3.1781-3.34550.26981360.26161256100
3.3455-3.55480.28341410.23981265100
3.5548-3.82890.25171370.21751241100
3.8289-4.21350.21271440.18511268100
4.2135-4.82150.18381440.16311251100
4.8215-6.06820.21721400.18531257100
6.0682-32.6010.181340.1755125299

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