[English] 日本語
Yorodumi
- PDB-7xzn: Formate-tetrahydrofolate ligase from Peptostreptococcus anaerobius -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more