[English] 日本語
Yorodumi
- PDB-5bj3: THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bj3
TitleTHERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1
ComponentsPROTEIN (ASPARTATE AMINOTRANSFERASE)
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL ENZYME
Function / homology
Function and homology information


aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Aspartate/prephenate aminotransferase
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsUra, H. / Nakai, T. / Kawaguchi, S.I. / Miyahara, I. / Hirotsu, K. / Kuramitsu, S.
CitationJournal: J.BIOCHEM.(TOKYO) / Year: 2001
Title: Substrate recognition mechanism of thermophilic dual-substrate enzyme
Authors: Ura, H. / Nakai, T. / Kawaguchi, S.I. / Miyahara, I. / Hirotsu, K. / Kuramitsu, S.
History
DepositionJan 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 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: PROTEIN (ASPARTATE AMINOTRANSFERASE)
B: PROTEIN (ASPARTATE AMINOTRANSFERASE)
C: PROTEIN (ASPARTATE AMINOTRANSFERASE)
D: PROTEIN (ASPARTATE AMINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,6088
Polymers168,6204
Non-polymers9894
Water5,999333
1
A: PROTEIN (ASPARTATE AMINOTRANSFERASE)
B: PROTEIN (ASPARTATE AMINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8044
Polymers84,3102
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-22 kcal/mol
Surface area25170 Å2
MethodPISA
2
C: PROTEIN (ASPARTATE AMINOTRANSFERASE)
D: PROTEIN (ASPARTATE AMINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8044
Polymers84,3102
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-21 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.440, 62.250, 154.770
Angle α, β, γ (deg.)90.00, 109.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
PROTEIN (ASPARTATE AMINOTRANSFERASE) / E.C.2.6.1.1 TRANSFERASE


Mass: 42154.969 Da / Num. of mol.: 4 / Mutation: S14D,T16P,K101S,S261R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / Strain (production host): AB1157 / References: UniProt: Q56232, aspartate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growpH: 4.3 / Details: CRYSTALLIZED FROM 30MM AMMONIUM PHOSPHATE, PH 4.3

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 77082 / % possible obs: 78.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.28 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3 / % possible all: 61.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJW

1bjw


Resolution: 2.2→8 Å / Rfactor Rfree error: 0.0028 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.243 7454 10 %RANDOM
Rwork0.215 ---
obs0.215 74025 77.4 %-
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11228 0 60 333 11621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.331.5
X-RAY DIFFRACTIONx_mcangle_it4.272
X-RAY DIFFRACTIONx_scbond_it5.942
X-RAY DIFFRACTIONx_scangle_it8.852.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 3.17 Å2 / Rms dev position: 0.076 Å / Weight Biso : 1 / Weight position: 500
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3112 710 10 %
Rwork0.2816 6487 -
obs--60.53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.PLPTOPHCSDX.PRO

+
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