[English] 日本語
Yorodumi
- PDB-1vl2: Crystal structure of Argininosuccinate synthase (TM1780) from The... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vl2
TitleCrystal structure of Argininosuccinate synthase (TM1780) from Thermotoga maritima at 1.65 A resolution
ComponentsArgininosuccinate synthase
KeywordsLIGASE / TM1780 / ARGININOSUCCINATE SYNTHASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


argininosuccinate metabolic process / argininosuccinate synthase / argininosuccinate synthase activity / urea cycle / arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Single helix bin / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. ...Single helix bin / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Argininosuccinate synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Argininosuccinate synthase (TM1780) from Thermotoga maritima at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 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: Argininosuccinate synthase
B: Argininosuccinate synthase
C: Argininosuccinate synthase
D: Argininosuccinate synthase


Theoretical massNumber of molelcules
Total (without water)190,3104
Polymers190,3104
Non-polymers00
Water21,3301184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23330 Å2
ΔGint-168 kcal/mol
Surface area53680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.322, 114.906, 149.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Argininosuccinate synthase / Citrulline--aspartate ligase


Mass: 47577.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: argG, TM1780 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X2A1, argininosuccinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1184 / 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: 2.16 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 16% PEG 3350, 0.20M Mg Acetate, 0.10M Imidazole , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Sep 20, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 195858 / % possible obs: 99.95 % / Redundancy: 4.91 % / Biso Wilson estimate: 25.36 Å2 / Rsym value: 0.073 / Net I/σ(I): 22.21
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.17 / Num. unique all: 19384 / Rsym value: 0.665 / % possible all: 99.87

-
Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KH1

1kh1


Resolution: 1.65→49.21 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.633 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 9757 5 %RANDOM
Rwork0.17742 ---
obs0.17902 185987 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.635 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12327 0 0 1184 13511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02212623
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211513
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.94917083
X-RAY DIFFRACTIONr_angle_other_deg1.345326725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95551562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48924.296568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.062152150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7431563
X-RAY DIFFRACTIONr_chiral_restr0.1080.21874
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022556
X-RAY DIFFRACTIONr_nbd_refined0.2240.22459
X-RAY DIFFRACTIONr_nbd_other0.1830.211617
X-RAY DIFFRACTIONr_nbtor_other0.0890.27029
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2854
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.220
X-RAY DIFFRACTIONr_mcbond_it2.3937974
X-RAY DIFFRACTIONr_mcbond_other0.60333204
X-RAY DIFFRACTIONr_mcangle_it3.295512526
X-RAY DIFFRACTIONr_scbond_it5.17585264
X-RAY DIFFRACTIONr_scangle_it7.419114557
LS refinement shellResolution: 1.65→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 689 4.91 %
Rwork0.239 13333 -
Refinement TLS params.Method: refined / Origin x: 47.7209 Å / Origin y: 1.7912 Å / Origin z: 39.0681 Å
111213212223313233
T-0.0169 Å20.0013 Å2-0.0007 Å2--0.0274 Å20.0007 Å2--0.0001 Å2
L0.0649 °20 °20.0181 °2-0.0618 °2-0.0254 °2--0.4162 °2
S-0.0141 Å °-0.0048 Å °-0.0047 Å °0.0003 Å °0.0065 Å °-0.0028 Å °-0.0048 Å °-0.0162 Å °0.0076 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA2 - 40914 - 421
2BB2 - 40914 - 421
3CC2 - 40414 - 416
4DD2 - 40414 - 416

+
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