[English] 日本語
Yorodumi
- PDB-5zn8: Crystal structure of nicotinamidase PncA from Bacillus subtilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zn8
TitleCrystal structure of nicotinamidase PncA from Bacillus subtilis
ComponentsIsochorismatase
KeywordsMETAL BINDING PROTEIN / Nicotinamidase / PncA / Bacillus subtilis
Function / homology
Function and homology information


Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine hydrolase / Cysteine hydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShang, F. / Chen, J. / Wang, L. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200556 China
National Natural Science Foundation of China21272031 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2018
Title: Crystal structure of the nicotinamidase/pyrazinamidase PncA from Bacillus subtilis.
Authors: Shang, F. / Chen, J. / Wang, L. / Jin, L. / Zou, L. / Bu, T. / Dong, Y. / Ha, N.C. / Nam, K.H. / Quan, C. / Xu, Y.
History
DepositionApr 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isochorismatase
B: Isochorismatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1714
Polymers41,0402
Non-polymers1312
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-88 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.037, 90.037, 86.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

-
Components

#1: Protein Isochorismatase / PncA


Mass: 20519.918 Da / Num. of mol.: 2 / Mutation: F5L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BMJ37_14840 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A2D3DSA4, UniProt: A0A223CGG0*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.39 M sodium citrate,0.1 M HEPES (pH 7.5)

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9826 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9826 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31118 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 30.2 Å2 / Rsym value: 0.074 / Net I/σ(I): 32.46
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.91 / Rsym value: 0.365 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O91

3o91


Resolution: 2→28.91 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2227 1699 6.35 %
Rwork0.1537 --
obs0.1581 26757 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 2 399 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122927
X-RAY DIFFRACTIONf_angle_d1.323965
X-RAY DIFFRACTIONf_dihedral_angle_d15.8831049
X-RAY DIFFRACTIONf_chiral_restr0.054433
X-RAY DIFFRACTIONf_plane_restr0.007523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.0590.27051360.21312066X-RAY DIFFRACTION100
2.059-2.12540.29531380.20182071X-RAY DIFFRACTION100
2.1254-2.20130.27311430.20552098X-RAY DIFFRACTION100
2.2013-2.28940.2841380.20122051X-RAY DIFFRACTION100
2.2894-2.39360.26431410.19312094X-RAY DIFFRACTION100
2.3936-2.51970.25471450.18162081X-RAY DIFFRACTION100
2.5197-2.67750.22431460.17122081X-RAY DIFFRACTION100
2.6775-2.8840.24411470.17242096X-RAY DIFFRACTION100
2.884-3.17390.21981380.15392103X-RAY DIFFRACTION100
3.1739-3.63250.21311450.14032099X-RAY DIFFRACTION100
3.6325-4.57360.18931450.1162093X-RAY DIFFRACTION100
4.5736-28.91320.18851370.13132125X-RAY DIFFRACTION99

+
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