[English] 日本語
Yorodumi
- PDB-1j1z: Crystal Structure of Thermus thermophilus HB8 Argininosuccinate S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j1z
TitleCrystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with substrate
ComponentsArgininosuccinate Synthetase
KeywordsLIGASE / ATP-binding / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate metabolic process / argininosuccinate synthase activity / urea cycle / L-arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthetase, catalytic/multimerisation domain body / : / : / Arginosuccinate synthase N-terminal HUP domain / Arginosuccinate synthase C-terminal domain ...Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthetase, catalytic/multimerisation domain body / : / : / Arginosuccinate synthase N-terminal HUP domain / Arginosuccinate synthase C-terminal domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / ADENOSINE-5'-TRIPHOSPHATE / CITRULLINE / Argininosuccinate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGoto, M. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structures of argininosuccinate synthetase in enzyme-ATP-substrates and enzyme-AMP-product forms
Authors: Goto, M. / Omi, R. / Miyahara, I. / Sugahara, M. / Hirotsu, K.
History
DepositionDec 24, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Argininosuccinate Synthetase
B: Argininosuccinate Synthetase
C: Argininosuccinate Synthetase
D: Argininosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,76616
Polymers179,5044
Non-polymers3,26212
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33200 Å2
ΔGint-111 kcal/mol
Surface area49230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.33, 229.33, 159.26
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
Argininosuccinate Synthetase


Mass: 44875.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P59846, argininosuccinate synthase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CIR / CITRULLINE


Type: L-peptide linking / Mass: 175.186 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13N3O3
#4: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 4.38 Å3/Da / Density % sol: 71.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: tris, ammonium sulfate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
22.4 Mammonium sulfate1reservoir
330 %(v/v)glycerol1reservoir
4100 mMTris-HCl1reservoirpH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 178320 / Num. obs: 178320 / % possible obs: 98.2 %
Reflection shellResolution: 2.1→2.17 Å / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. measured all: 561786 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.7

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→10 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.257 17293 RANDOM
Rwork0.226 --
all-178320 -
obs-173798 -
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12264 0 208 678 13150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.427
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.2571 / Rfactor Rwork: 0.2327
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.43
LS refinement shell
*PLUS
Rfactor Rfree: 0.3392 / Rfactor Rwork: 0.3034

+
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