[English] 日本語
Yorodumi
- PDB-7p4p: Structure of the quinolinate synthase A84L variant complexed with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p4p
TitleStructure of the quinolinate synthase A84L variant complexed with citrate
ComponentsQuinolinate synthase A
KeywordsTRANSFERASE / NAD biosynthesis / Iron Sulfur cluster / active site cavity
Function / homology
Function and homology information


quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD biosynthetic process from aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Quinolinate synthetase A / Quinolinate synthase A, type 2 / Quinolinate synthetase A superfamily / Quinolinate synthetase A protein
Similarity search - Domain/homology
CITRATE ANION / IRON/SULFUR CLUSTER / Quinolinate synthase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVolbeda, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE18-0026 France
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA.
Authors: Basbous, H. / Volbeda, A. / Amara, P. / Rohac, R. / Martin, L. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C.
History
DepositionJul 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Quinolinate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3707
Polymers34,6991
Non-polymers6716
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-47 kcal/mol
Surface area13320 Å2
Unit cell
Length a, b, c (Å)102.760, 49.200, 69.680
Angle α, β, γ (deg.)90.000, 108.080, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

21A-736-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Quinolinate synthase A


Mass: 34698.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: nadA, TM_1644
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9X1X7, quinolinate synthase

-
Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: trisodium citrate, Tris-HCL, KCL, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.75→48.84 Å / Num. obs: 33318 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 28.77 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.5
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.888 / Num. unique obs: 3180 / CC1/2: 0.643

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lqm

5lqm


Resolution: 1.75→39.23 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1651 4.96 %
Rwork0.1706 31659 -
obs0.1723 33310 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.49 Å2 / Biso mean: 35.6935 Å2 / Biso min: 16.27 Å2
Refinement stepCycle: final / Resolution: 1.75→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 25 351 2774
Biso mean--28.26 44.88 -
Num. residues----305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.80.32931160.29272553266997
1.8-1.860.2771370.252426432780100
1.86-1.930.28071140.234926742788100
1.93-20.2971370.229626052742100
2-2.090.21841470.193426472794100
2.09-2.20.22111290.183526602789100
2.2-2.340.22781250.183426622787100
2.34-2.520.22481470.181726322779100
2.52-2.780.20471570.179726292786100
2.78-3.180.21131450.17822656280199
3.18-40.17021490.14152611276098
4.01-39.230.171480.14172687283598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.26870.0987-0.55960.83-0.51960.8041-0.03190.32880.0513-0.17610.2950.28230.1822-0.5495-0.0230.1911-0.0547-0.05140.39920.12610.28678.4371-2.81316.2342
20.5568-0.02350.33310.299-0.0690.4877-0.0335-0.00160.0345-0.010.02280.01210.03840.123-00.2230.0083-0.00530.2155-0.00030.218330.28466.08729.2168
30.24410.0126-0.21080.592-0.12450.3580.04090.04870.0285-0.2118-0.0196-0.08070.10970.111600.25980.00260.02420.22620.00690.22430.39320.21794.4645
40.08750.0462-0.03950.1869-0.16940.143-0.07910.07990.0876-0.04940.23510.06150.3424-0.29480.01360.3402-0.1573-0.02820.40970.05990.30318.2523-11.641919.5121
50.04720.0240.02480.06160.06080.0551-0.0423-0.12640.21840.18210.0280.3831-0.2074-0.19410.00020.29810.07440.05060.277-0.01110.375915.680310.774730.9066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 81 )A-6 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 168 )A82 - 168
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 254 )A169 - 254
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 278)A255 - 278
5X-RAY DIFFRACTION5chain 'A' and (resid 279 through 298)A279 - 298

+
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