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- PDB-7xzn: Formate-tetrahydrofolate ligase from Peptostreptococcus anaerobius -

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Basic information

Entry
Database: PDB / ID: 7xzn
TitleFormate-tetrahydrofolate ligase from Peptostreptococcus anaerobius
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
Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesPeptostreptococcus anaerobius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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)243,60618
Polymers242,3334
Non-polymers1,27414
Water2,108117
1
A: Formate--tetrahydrofolate ligase
C: Formate--tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,92711
Polymers121,1662
Non-polymers7619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-13 kcal/mol
Surface area38810 Å2
MethodPISA
2
B: Formate--tetrahydrofolate ligase
D: Formate--tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6797
Polymers121,1662
Non-polymers5135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-17 kcal/mol
Surface area38920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.870, 116.300, 107.380
Angle α, β, γ (deg.)90.000, 92.580, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 50 or (resid 51...
21(chain B and (resid 4 through 25 or (resid 26...
31(chain C and (resid 4 through 13 or (resid 14...
41(chain D and (resid 4 through 13 or (resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTHRTHR(chain A and (resid 4 through 50 or (resid 51...AA4 - 508 - 54
12LYSLYSLYSLYS(chain A and (resid 4 through 50 or (resid 51...AA5155
13LYSLYSPHEPHE(chain A and (resid 4 through 50 or (resid 51...AA4 - 5588 - 562
14LYSLYSPHEPHE(chain A and (resid 4 through 50 or (resid 51...AA4 - 5588 - 562
15LYSLYSPHEPHE(chain A and (resid 4 through 50 or (resid 51...AA4 - 5588 - 562
16LYSLYSPHEPHE(chain A and (resid 4 through 50 or (resid 51...AA4 - 5588 - 562
21LYSLYSILEILE(chain B and (resid 4 through 25 or (resid 26...BB4 - 258 - 29
22ASNASNASNASN(chain B and (resid 4 through 25 or (resid 26...BB2630
23PHEPHEPHEPHE(chain B and (resid 4 through 25 or (resid 26...BB3 - 5587 - 562
24PHEPHEPHEPHE(chain B and (resid 4 through 25 or (resid 26...BB3 - 5587 - 562
25PHEPHEPHEPHE(chain B and (resid 4 through 25 or (resid 26...BB3 - 5587 - 562
26PHEPHEPHEPHE(chain B and (resid 4 through 25 or (resid 26...BB3 - 5587 - 562
31LYSLYSALAALA(chain C and (resid 4 through 13 or (resid 14...CC4 - 138 - 17
32ASNASNASNASN(chain C and (resid 4 through 13 or (resid 14...CC1418
33PHEPHEPHEPHE(chain C and (resid 4 through 13 or (resid 14...CC3 - 5587 - 562
34PHEPHEPHEPHE(chain C and (resid 4 through 13 or (resid 14...CC3 - 5587 - 562
35PHEPHEPHEPHE(chain C and (resid 4 through 13 or (resid 14...CC3 - 5587 - 562
36ASNASNASNASN(chain C and (resid 4 through 13 or (resid 14...CC2630
37ASNASNASNASN(chain C and (resid 4 through 13 or (resid 14...CC2630
38PHEPHEPHEPHE(chain C and (resid 4 through 13 or (resid 14...CC3 - 5587 - 562
39PHEPHEPHEPHE(chain C and (resid 4 through 13 or (resid 14...CC3 - 5587 - 562
310PHEPHEPHEPHE(chain C and (resid 4 through 13 or (resid 14...CC3 - 5587 - 562
311PHEPHEPHEPHE(chain C and (resid 4 through 13 or (resid 14...CC3 - 5587 - 562
41LYSLYSALAALA(chain D and (resid 4 through 13 or (resid 14...DD4 - 138 - 17
42ASNASNASNASN(chain D and (resid 4 through 13 or (resid 14...DD1418
43PHEPHELEULEU(chain D and (resid 4 through 13 or (resid 14...DD3 - 5577 - 561
44PHEPHELEULEU(chain D and (resid 4 through 13 or (resid 14...DD3 - 5577 - 561
45PHEPHELEULEU(chain D and (resid 4 through 13 or (resid 14...DD3 - 5577 - 561
46PHEPHELEULEU(chain D and (resid 4 through 13 or (resid 14...DD3 - 5577 - 561

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.15M Cesium chloride, 15% w/v PEG 3350

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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: 2.04→54.02 Å / Num. obs: 168145 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 8
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 7.2 % / Num. unique obs: 12394 / CC1/2: 0.617 / % possible all: 100

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Processing

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

5a4j


Resolution: 2.04→30.5 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 37.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 2003 1.19 %
Rwork0.2715 165857 -
obs0.2716 167860 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.16 Å2 / Biso mean: 54.4083 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 2.04→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16630 0 84 117 16831
Biso mean--63.03 36.39 -
Num. residues----2222
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10386X-RAY DIFFRACTION7.961TORSIONAL
12B10386X-RAY DIFFRACTION7.961TORSIONAL
13C10386X-RAY DIFFRACTION7.961TORSIONAL
14D10386X-RAY DIFFRACTION7.961TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.04-2.0910.41481380.387211764100
2.091-2.14750.44281460.368611878100
2.1475-2.21070.41531330.346311798100
2.2107-2.2820.34371510.334711843100
2.282-2.36360.38361470.325811815100
2.3636-2.45820.35541430.315711807100
2.4582-2.570.31241410.312411840100
2.57-2.70540.35661410.302311813100
2.7054-2.87480.32551560.295111813100
2.8748-3.09660.31821390.305411865100
3.0966-3.40780.27951460.278411877100
3.4078-3.90010.2861430.254711869100
3.9001-4.91030.20741380.209211936100
4.9103-30.50.19481410.22971193999

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