[English] 日本語
Yorodumi
- PDB-7wrp: Crystal Structure of pks13-ACP domain from Corynebacterium diphtheriae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wrp
TitleCrystal Structure of pks13-ACP domain from Corynebacterium diphtheriae
ComponentsPolyketide synthase involved in mycolic acid biosynthesis
KeywordsRECOMBINATION / acyl-carrier protein
Function / homology4'-PHOSPHOPANTETHEINE / Polyketide synthase involved in mycolic acid biosynthesis
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsLiu, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of FadD32 and pks13-ACP domain from Corynebacterium diphtheriae.
Authors: Chen, R. / Yuan, J. / Shi, X. / Tang, W. / Liu, X.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Polyketide synthase involved in mycolic acid biosynthesis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7082
Polymers9,3501
Non-polymers3581
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-2 kcal/mol
Surface area4800 Å2
Unit cell
Length a, b, c (Å)48.886, 48.886, 111.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Polyketide synthase involved in mycolic acid biosynthesis


Mass: 9349.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Corynebacterium diphtheriae (bacteria) / References: UniProt: A0A806GVW0
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.59 % / Mosaicity: 0.83 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8
Details: 0.2 M (NH4)2SO4, 0.1 M NaAc??3H2O pH 4.6, 25% w/v PEG 4,000, VAPOR DIFFUSION, Sitting DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9784 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.794→50 Å / Num. obs: 13451 / % possible obs: 100 % / Redundancy: 22.2 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.028 / Rrim(I) all: 0.125 / Χ2: 1.209 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.8-1.8324.30.5916670.9540.1220.6030.917
1.83-1.8624.80.5236500.9660.1070.5341.023
1.86-1.924.40.4996350.9580.1030.511.119
1.9-1.9424.20.4666710.9590.0960.4751.113
1.94-1.9823.70.4086470.9680.0860.4171.215
1.98-2.0323.30.3546580.9780.0760.3621.289
2.03-2.0821.10.3236540.9840.0730.3321.368
2.08-2.1323.20.2846590.9830.0620.2911.427
2.13-2.223.70.2636520.9850.0560.271.383
2.2-2.2723.70.2516600.9890.0540.2561.354
2.27-2.3522.60.2286720.9910.050.2331.347
2.35-2.4421.90.2076620.9870.0460.2121.316
2.44-2.5520.30.1796650.9910.0420.1841.236
2.55-2.69220.1626680.9930.0360.1661.266
2.69-2.8621.90.1496700.9950.0330.1521.148
2.86-3.0821.20.1316810.9950.030.1351.225
3.08-3.3919.20.1186760.9970.0280.1211.175
3.39-3.8820.90.1037010.9960.0240.1060.989
3.88-4.8819.60.0957170.9970.0220.0981.185
4.88-5019.40.0957860.9970.0230.0981.131

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6c4q

6c4q


Resolution: 1.794→34.568 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 617 4.61 %
Rwork0.1956 12767 -
obs0.1965 13384 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.98 Å2 / Biso mean: 37.7649 Å2 / Biso min: 20.32 Å2
Refinement stepCycle: final / Resolution: 1.794→34.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms602 0 43 90 735
Biso mean--61.99 45.5 -
Num. residues----78
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.794-1.97410.2511480.22163102
1.9741-2.25970.28171310.20733147
2.2597-2.84670.23951680.22113164
2.8467-34.5680.19171700.18163354

+
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