[English] 日本語
Yorodumi
- PDB-1ock: THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ock
TitleTHE CRYSTAL STRUCTURE OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
ComponentsMALONAMIDASE E2
KeywordsAMIDASE / MALONAMIDASE
Function / homology
Function and homology information


Amidase / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesBRADYRHIZOBIUM JAPONICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsShin, S. / Ha, N.-C. / Lee, T.-H. / Oh, B.-H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Characterization of a Novel Ser-Cisser-Lys Catalytic Triad in Comparison with the Classical Ser-His-Asp Triad.
Authors: Shin, S. / Yun, Y.S. / Koo, H.M. / Kim, Y.S. / Choi, K.Y. / Oh, B.-H.
History
DepositionFeb 8, 2003Deposition site: PDBE / Processing site: PDBE
SupersessionMar 3, 2003ID: 1GR8
Revision 1.0Mar 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MALONAMIDASE E2
B: MALONAMIDASE E2


Theoretical massNumber of molelcules
Total (without water)87,1832
Polymers87,1832
Non-polymers00
Water16,916939
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.287, 95.581, 74.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein MALONAMIDASE E2


Mass: 43591.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CIS PEPTIDE BOND BETWEEN GLY 130 AND SER 131 / Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Plasmid: PUC18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: Q9ZIV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYZES MALONAMATE (-OOCCH2CONH2) INTO MALONATE AND AMMONIA. INVOLVED IN THE TRANSPORT OF FIXED ...HYDROLYZES MALONAMATE (-OOCCH2CONH2) INTO MALONATE AND AMMONIA. INVOLVED IN THE TRANSPORT OF FIXED NITROGEN FROM BACTEROIDS TO PLANT CELLS IN SYMBIOTIC NITROGEN METABOLISM
Sequence detailsTHE RESIDUES 401-412 DIFFER FROM THAT IN THE SWISS-PROT ENTRY Q9ZIV5 DUE TO FRAME SHIFT BECAUSE OF ...THE RESIDUES 401-412 DIFFER FROM THAT IN THE SWISS-PROT ENTRY Q9ZIV5 DUE TO FRAME SHIFT BECAUSE OF ADDITION OF ADENINE 1202 IN THE ORIGINAL SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39.9 %
Crystal growpH: 7 / Details: 20% POLYETHYLENE GLYCOL 1000, 100 MM TRIS, PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 68327 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.037 / Net I/σ(I): 41.76
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Mean I/σ(I) obs: 9.81 / Rsym value: 0.113 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / Rfactor Rfree error: 6.5E-5 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3477 5 %RANDOM
Rwork0.19 ---
obs0.19 68274 97.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.755 Å20 Å20 Å2
2---5.201 Å20 Å2
3---0.446 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 0 939 7065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0049
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.276
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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://pdbjlvh1.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