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- PDB-7c11: Formate--tetrahydrofolate ligase from Methylobacterium extorquens... -

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Basic information

Entry
Database: PDB / ID: 7c11
TitleFormate--tetrahydrofolate ligase from Methylobacterium extorquens CM4 strain
ComponentsFormate-tetrahydrofolate ligaseFormate–tetrahydrofolate ligase
KeywordsLIGASE / Formate assimilation / Methylobacterium extorquens CM4 / formate-tetrahydrofolate ligase / metal usage
Function / homology
Function and homology information


formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / tetrahydrofolate interconversion / ATP binding
Similarity search - Function
Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / CITRATE ANION / L(+)-TARTARIC ACID / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.815 Å
AuthorsKim, K.-J. / Kim, S. / Seo, H. / Lee, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Biochemical properties and crystal structure of formate-tetrahydrofolate ligase from Methylobacterium extorquens CM4.
Authors: Kim, S. / Lee, S.H. / Seo, H. / Kim, K.J.
History
DepositionMay 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formate-tetrahydrofolate ligase
B: Formate-tetrahydrofolate ligase
C: Formate-tetrahydrofolate ligase
D: Formate-tetrahydrofolate ligase
M: Formate-tetrahydrofolate ligase
N: Formate-tetrahydrofolate ligase
O: Formate-tetrahydrofolate ligase
P: Formate-tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,12411
Polymers486,7268
Non-polymers3983
Water6,846380
1
A: Formate-tetrahydrofolate ligase
B: Formate-tetrahydrofolate ligase
C: Formate-tetrahydrofolate ligase
D: Formate-tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,5726
Polymers243,3634
Non-polymers2092
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-74 kcal/mol
Surface area73890 Å2
MethodPISA
2
M: Formate-tetrahydrofolate ligase
N: Formate-tetrahydrofolate ligase
O: Formate-tetrahydrofolate ligase
P: Formate-tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,5525
Polymers243,3634
Non-polymers1891
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-69 kcal/mol
Surface area73500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.563, 168.742, 126.991
Angle α, β, γ (deg.)90.000, 100.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Formate-tetrahydrofolate ligase / Formate–tetrahydrofolate ligase / Formyltetrahydrofolate synthetase / FTHFS


Mass: 60840.766 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (strain CM4 / NCIMB 13688) (bacteria)
Strain: CM4 / NCIMB 13688 / Gene: fhs, Mchl_0447 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: B7L0A5, formate-tetrahydrofolate ligase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion
Details: 20% PEG 3350, 2% tacsimate pH 6.0, 0.1M bis-tris pH 6.5

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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: 2.8→50 Å / Num. obs: 102924 / % possible obs: 99 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.082 / Rrim(I) all: 0.143 / Χ2: 2.454 / Net I/σ(I): 8.6 / Num. measured all: 287673
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.70.33150980.7670.2410.4111.40998.8
2.85-2.92.70.30751590.8020.2240.3811.49399.2
2.9-2.962.70.28150990.8360.2040.3491.50999
2.96-3.022.70.25951470.80.1880.3221.69799.1
3.02-3.082.70.22851510.8830.1660.2831.61399.1
3.08-3.152.70.21851180.8940.1570.2691.81799.1
3.15-3.232.70.19151410.9190.1370.2361.95199.2
3.23-3.322.70.17351370.9310.1230.2132.14399.3
3.32-3.422.80.15651680.9450.1110.1932.29899.3
3.42-3.532.80.14151480.9530.10.1732.37199.3
3.53-3.652.80.12851300.9610.090.1572.63399.3
3.65-3.82.80.11451690.9680.080.1392.61299.3
3.8-3.972.90.10351380.9740.0720.1272.64899.2
3.97-4.182.90.09551660.9790.0660.1162.88199.1
4.18-4.442.90.08751440.9790.0610.1072.89699.2
4.44-4.792.90.08551770.980.0590.1042.99699.1
4.79-5.272.90.08551570.9790.0590.1042.92599.1
5.27-6.032.90.08551560.980.0590.1042.49399.1
6.03-7.592.90.08151710.9840.0550.0982.73398.6
7.59-502.80.08451500.980.0580.1035.37896.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A4J

5a4j


Resolution: 2.815→36.6 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.846 / SU B: 18.747 / SU ML: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 5124 5 %RANDOM
Rwork0.1799 ---
obs0.1847 97775 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.64 Å2 / Biso mean: 39.596 Å2 / Biso min: 7.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-0.56 Å2
2---0.33 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 2.815→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33258 0 27 380 33665
Biso mean--47.87 27.15 -
Num. residues----4437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01333845
X-RAY DIFFRACTIONr_bond_other_d0.0010.01732654
X-RAY DIFFRACTIONr_angle_refined_deg1.631.63645814
X-RAY DIFFRACTIONr_angle_other_deg1.1971.57775556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64654427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88922.2821586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02155786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.71315216
X-RAY DIFFRACTIONr_chiral_restr0.0630.24578
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0238182
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026714
LS refinement shellResolution: 2.815→2.888 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.336 324 -
Rwork0.228 5677 -
obs--77.3 %

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