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- PDB-7xzo: Formate-tetrahydrofolate ligase in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 7xzo
TitleFormate-tetrahydrofolate ligase in complex with ATP
ComponentsFormate--tetrahydrofolate ligase
KeywordsLIGASE / Formate tetrahydrofolate ligase / ATP
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
ADENOSINE-5'-TRIPHOSPHATE / (R,R)-2,3-BUTANEDIOL / : / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesPeptostreptococcus anaerobius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsFang, C.L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Bmc Biol. / Year: 2023
Title: Identification of FtfL as a novel target of berberine in intestinal bacteria.
Authors: Yan, J. / Fang, C. / Yang, G. / Li, J. / Liu, Y. / Zhang, L. / Yang, P. / Fang, J. / Gu, Y. / Zhang, Y. / Jiang, W.
History
DepositionJun 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,96817
Polymers242,3334
Non-polymers2,63613
Water1,36976
1
A: Formate--tetrahydrofolate ligase
C: Formate--tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2596
Polymers121,1662
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-36 kcal/mol
Surface area37610 Å2
MethodPISA
2
B: Formate--tetrahydrofolate ligase
D: Formate--tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,70911
Polymers121,1662
Non-polymers1,5439
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-23 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.280, 115.100, 106.530
Angle α, β, γ (deg.)90.000, 93.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 60583.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptostreptococcus anaerobius (bacteria)
Gene: fhs, NCTC11460_01517 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A379CIH2, formate-tetrahydrofolate ligase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG 3350, 200mM potassium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.31→32.48 Å / Num. obs: 113515 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.995 / Net I/σ(I): 5.6
Reflection shellResolution: 2.31→2.37 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8382 / CC1/2: 0.523 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5a4j

5a4j


Resolution: 2.31→30.029 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 34.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2899 1978 1.75 %
Rwork0.2524 111301 -
obs0.253 113279 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.84 Å2 / Biso mean: 42.4203 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: final / Resolution: 2.31→30.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16768 0 158 76 17002
Biso mean--57.93 30.28 -
Num. residues----2232
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.31-2.36780.33621510.3367903100
2.3678-2.43170.41041360.33827916100
2.4317-2.50330.33771450.32977937100
2.5033-2.5840.32271470.32597909100
2.584-2.67630.38881290.31827972100
2.6763-2.78340.31931430.30387924100
2.7834-2.910.31091380.28917956100
2.91-3.06330.34871450.28487949100
3.0633-3.2550.30961500.27427908100
3.255-3.50590.28391420.24857977100
3.5059-3.85810.2981380.22277958100
3.8581-4.41490.24751380.21237987100
4.4149-5.55650.24091380.20648014100
5.5565-300.22861380.2042799198

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