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- PDB-7vg4: 10,5-methenyltetrahydrofolate cyclohydrolase from Methylobacteriu... -

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Basic information

Entry
Database: PDB / ID: 7vg4
Title10,5-methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1 strain
ComponentsMethenyltetrahydrofolate cyclohydrolase
KeywordsHYDROLASE / Methylobacterium extorquens AM1 / Tetrahydrofolate cycle / Formate assimilation / 5 / 10-Methenyltetrahydrofolate cyclohydrolase
Function / homology: / Cyclodeaminase/cyclohydrolase / Formimidoyltransferase-cyclodeaminase-like superfamily / Formiminotransferase-cyclodeaminase / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / one-carbon metabolic process / membrane / Methenyltetrahydrofolate cyclohydrolase
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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
C: Methenyltetrahydrofolate cyclohydrolase
D: Methenyltetrahydrofolate cyclohydrolase
E: Methenyltetrahydrofolate cyclohydrolase
F: Methenyltetrahydrofolate cyclohydrolase


Theoretical massNumber of molelcules
Total (without water)136,9026
Polymers136,9026
Non-polymers00
Water1,09961
1
A: Methenyltetrahydrofolate cyclohydrolase
B: Methenyltetrahydrofolate cyclohydrolase


Theoretical massNumber of molelcules
Total (without water)45,6342
Polymers45,6342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-36 kcal/mol
Surface area17220 Å2
MethodPISA
2
C: Methenyltetrahydrofolate cyclohydrolase
D: Methenyltetrahydrofolate cyclohydrolase


Theoretical massNumber of molelcules
Total (without water)45,6342
Polymers45,6342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-36 kcal/mol
Surface area17360 Å2
MethodPISA
3
E: Methenyltetrahydrofolate cyclohydrolase
F: Methenyltetrahydrofolate cyclohydrolase


Theoretical massNumber of molelcules
Total (without water)45,6342
Polymers45,6342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-37 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.743, 67.730, 88.586
Angle α, β, γ (deg.)80.140, 79.310, 79.420
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Methenyltetrahydrofolate cyclohydrolase


Mass: 22816.965 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tacsimate, Sodium acetate trihydrate

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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: Oct 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 28658 / % possible obs: 96.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.069 / Rrim(I) all: 0.098 / Χ2: 2.831 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.851.80.25413790.8740.2540.362.03693.2
2.85-2.91.80.24614200.8710.2460.3482.23296.2
2.9-2.961.80.22914110.9110.2290.3232.10594
2.96-3.021.80.21314090.9160.2130.3012.22395.4
3.02-3.081.90.19314050.9280.1930.2732.30795.9
3.08-3.151.80.16714240.9420.1670.2372.38295.2
3.15-3.231.90.15214220.9490.1520.2152.27496.2
3.23-3.321.90.13313970.9650.1330.1882.51296.3
3.32-3.421.90.10814580.9750.1080.1522.67496
3.42-3.531.90.10314360.9770.1030.1452.82697.9
3.53-3.651.90.08914110.9810.0890.1262.97697.4
3.65-3.81.90.07514760.9830.0750.1073.50498.1
3.8-3.971.90.0714450.9870.070.0993.25998.6
3.97-4.181.90.05514680.990.0550.0782.96497.9
4.18-4.441.90.05114450.990.0510.0723.69998.6
4.44-4.791.90.04614370.9920.0460.0654.00398.2
4.79-5.271.90.04814870.9920.0480.0682.77198.7
5.27-6.031.90.05114550.9910.0510.0722.39898.8
6.03-7.591.90.04414610.9910.0440.0622.96499.1
7.59-501.80.04314120.9860.0430.064.31295.5

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Processing

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

1o5h


Resolution: 2.77→30.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.879 / SU B: 20.535 / SU ML: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2859 1405 4.9 %RANDOM
Rwork0.1959 ---
obs0.2004 27232 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.83 Å2 / Biso mean: 52.788 Å2 / Biso min: 20.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20.93 Å2-1.11 Å2
2---2.13 Å25.57 Å2
3---5.34 Å2
Refinement stepCycle: final / Resolution: 2.77→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8744 0 0 61 8805
Biso mean---37.86 -
Num. residues----1201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158786
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.63111873
X-RAY DIFFRACTIONr_angle_other_deg1.2161.58220208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34451190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97823.376394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.877151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9841554
X-RAY DIFFRACTIONr_chiral_restr0.0580.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021758
LS refinement shellResolution: 2.773→2.845 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 58 -
Rwork0.271 1395 -
all-1453 -
obs--64.58 %

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