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

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Basic information

Entry
Database: PDB / ID: 7wmx
TitleCrystal structure of methylenetetrahydrofolate reductase MSMEG_6649 from Mycobacterium smegmatis with 5,10-methylenetetrahydrofolate
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: 2.264 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
Water1,72996
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 area13730 Å2
Unit cell
Length a, b, c (Å)85.667, 85.667, 105.262
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.: 96 / 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: 3.38 Å3/Da / Density % sol: 63.62 %
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: 2.26→74.19 Å / Num. obs: 21276 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.05 / Rrim(I) all: 0.179 / Net I/σ(I): 12.1 / Num. measured all: 261414 / Scaling rejects: 11
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
2.26-2.3912.31.233747430580.760.361.2832.599.7
7.16-74.1911.70.07487887540.9960.0220.07829.899.9

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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: 2.264→42.926 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1051 4.95 %
Rwork0.1917 20195 -
obs0.1937 21246 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.6 Å2 / Biso mean: 44.859 Å2 / Biso min: 19.3 Å2
Refinement stepCycle: final / Resolution: 2.264→42.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 0 96 2378
Biso mean---48.49 -
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 (%)
2.2644-2.36740.26271410.2369245599
2.3674-2.49220.28041120.22482510100
2.4922-2.64840.26251150.22122501100
2.6484-2.85280.29551430.21932484100
2.8528-3.13980.27621330.21032512100
3.1398-3.59390.22791160.18982552100
3.5939-4.52720.18471570.15792514100
4.5272-42.9260.21921340.18382667100

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