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- PDB-7xzp: Formate-tetrahydrofolate ligase in complex with berberine -

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Basic information

Entry
Database: PDB / ID: 7xzp
TitleFormate-tetrahydrofolate ligase in complex with berberine
ComponentsFormate--tetrahydrofolate ligase
KeywordsLIGASE / Formate tetrahydrofolate ligase / Berberine
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
BERBERINE / PROLINE / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesPeptostreptococcus anaerobius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,74017
Polymers121,1662
Non-polymers2,57415
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-55 kcal/mol
Surface area39820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.260, 205.210, 107.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 60583.137 Da / Num. of mol.: 2
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-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H18NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 2.0M Ammonium sulfate

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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: 2.56→50.2 Å / Num. obs: 48875 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.978 / Rpim(I) all: 0.124 / Rrim(I) all: 0.339 / Χ2: 1.02 / Net I/σ(I): 8.8
Reflection shellResolution: 2.56→2.63 Å / Redundancy: 8.2 % / Num. unique obs: 3564 / CC1/2: 0.288 / % possible all: 100

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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: 2.56→47.651 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 2000 4.1 %
Rwork0.2013 46808 -
obs0.2027 48808 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.68 Å2 / Biso mean: 54.6661 Å2 / Biso min: 27.49 Å2
Refinement stepCycle: final / Resolution: 2.56→47.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8357 0 110 53 8520
Biso mean--63.22 47.68 -
Num. residues----1125
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.56-2.6240.35471420.32443305100
2.624-2.6950.32661400.30383291100
2.695-2.77420.35091410.3013309100
2.7742-2.86380.37121410.28743303100
2.8638-2.96610.32241410.27973310100
2.9661-3.08490.33271430.28623343100
3.0849-3.22520.29891410.25583293100
3.2252-3.39520.29861420.23483327100
3.3952-3.60790.23471430.21923344100
3.6079-3.88630.24261430.18763354100
3.8863-4.27720.19251430.16113344100
4.2772-4.89560.17541440.14053379100
4.8956-6.16580.20061450.17063405100
6.1658-47.650.16791510.1594350199

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