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- PDB-7vg5: 10,5-methenyltetrahydrofolate cyclohydrolase from Methylobacteriu... -

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Basic information

Entry
Database: PDB / ID: 7vg5
Title10,5-methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1 with tetrahydrofolate
ComponentsMethenyltetrahydrofolate cyclohydrolase
KeywordsHYDROLASE / Methylobacterium extorquens AM1 / Tetrahydrofolate cycle / Formate assimilation / 5 / 10-Methenyltetrahydrofolate cyclohydrolase
Function / homology
Function and homology information


methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / one-carbon metabolic process / membrane
Similarity search - Function
: / Cyclodeaminase/cyclohydrolase / Formimidoyltransferase-cyclodeaminase-like superfamily / Formiminotransferase-cyclodeaminase
Similarity search - Domain/homology
(6S)-5,6,7,8-TETRAHYDROFOLATE / Methenyltetrahydrofolate cyclohydrolase
Similarity search - Component
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKim, S. / Lee, S. / Kim, I.-K. / Seo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning (MSIP)2021M3D3A1A01079480_2021-5 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structural insight into a molecular mechanism of methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1.
Authors: Kim, S. / Lee, S.H. / Kim, I.K. / Seo, H. / Kim, K.J.
History
DepositionSep 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methenyltetrahydrofolate cyclohydrolase
B: Methenyltetrahydrofolate cyclohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5254
Polymers45,6342
Non-polymers8912
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, 54 kDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-26 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.322, 49.513, 64.071
Angle α, β, γ (deg.)90.000, 97.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methenyltetrahydrofolate cyclohydrolase


Mass: 22816.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: fchA, MexAM1_META1p1729 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q49135, methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, magnesium chloride hexahydrate, BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 18336 / % possible obs: 97.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.077 / Rrim(I) all: 0.142 / Χ2: 5.334 / Net I/σ(I): 14.3 / Num. measured all: 54337
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.292.50.3088770.6560.2230.3822.1496.1
2.29-2.332.50.2939110.6840.2110.3632.15897.3
2.33-2.382.60.2719060.7180.1930.3342.65197.6
2.38-2.422.60.2518850.7590.1830.3122.39695.9
2.42-2.482.70.239190.8360.1590.2812.47897.8
2.48-2.532.70.2258710.8330.1610.2782.90996.5
2.53-2.62.70.219340.8650.1460.2573.12797
2.6-2.672.80.1798830.9040.1210.2173.49696.6
2.67-2.752.90.1659140.9260.1140.2013.61496.9
2.75-2.832.90.1779000.9070.1190.2144.38498
2.83-2.942.90.1559330.9540.1030.1874.59898.6
2.94-3.0530.1489270.9310.0970.1785.14399.1
3.05-3.193.10.1359190.9430.0880.1625.22298.2
3.19-3.363.20.1239400.9620.080.1475.93198.8
3.36-3.573.30.1159170.970.0720.1367.40499.3
3.57-3.853.40.1169390.9720.0720.1378.83399.9
3.85-4.233.40.0979480.9840.060.1148.58799.4
4.23-4.853.40.0859500.9850.0530.18.1599.8
4.85-6.13.30.0959410.9620.0610.1136.83199.4
6.1-503.20.0969220.970.0640.1168.95492.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5H

1o5h


Resolution: 2.25→31.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.876 / SU B: 7.108 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 903 4.9 %RANDOM
Rwork0.1902 ---
obs0.1936 17433 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.87 Å2 / Biso mean: 33.91 Å2 / Biso min: 16.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0 Å2-0.45 Å2
2---0.33 Å2-0 Å2
3---1.84 Å2
Refinement stepCycle: final / Resolution: 2.25→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 26 18 3028
Biso mean--39.82 30.49 -
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173016
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.6344098
X-RAY DIFFRACTIONr_angle_other_deg1.3771.5836938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1885406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56723.433134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48515538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7891518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
LS refinement shellResolution: 2.254→2.313 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 56 -
Rwork0.236 1231 -
all-1287 -
obs--94.7 %

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