[English] 日本語
Yorodumi
- PDB-1kxj: The Crystal Structure of Glutamine Amidotransferase from Thermoto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kxj
TitleThe Crystal Structure of Glutamine Amidotransferase from Thermotoga maritima
ComponentsAmidotransferase hisH
KeywordsTRANSFERASE / alpha-beta-alpha / Structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / histidine biosynthetic process / glutaminase activity / glutamine metabolic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKorolev, S. / Skarina, T. / Evdokimova, E. / Beasley, S. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of glutamine amidotransferase from Thermotoga maritima
Authors: Korolev, S. / Skarina, T. / Evdokimova, E. / Beasley, S. / Edwards, A. / Joachimiak, A. / Savchenko, A.
History
DepositionJan 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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: Amidotransferase hisH
B: Amidotransferase hisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5108
Polymers46,9402
Non-polymers5706
Water0
1
A: Amidotransferase hisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8505
Polymers23,4701
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amidotransferase hisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6603
Polymers23,4701
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.045, 82.045, 176.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Amidotransferase hisH / Glutamine amidotransferase


Mass: 23469.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HISH / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9X0C8, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 M mono-Ammonium dihydrogen Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 Mmono-ammonium dihydrogen phosphate1reservoir
2100 mMTris-HCl1reservoirpH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97916, 0.97938
DetectorType: SBC-2 / Detector: CCD / Date: Oct 1, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979161
20.979381
ReflectionResolution: 2.8→50 Å / Num. all: 32704 / Num. obs: 32696 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3245 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 99.3 %

-
Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data reduction
SnBphasing
SOLVEphasing
RESOLVEmodel building
Omodel building
CNS1.1refinement
d*TREKdata reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→39.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 115752.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1576 5.1 %RANDOM
Rwork0.229 ---
obs0.229 30941 94.6 %-
all-32704 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.7487 Å2 / ksol: 0.362597 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.38 Å28.12 Å20 Å2
2--6.38 Å20 Å2
3----12.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 30 0 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.392.5
X-RAY DIFFRACTIONc_mcangle_it3.843
X-RAY DIFFRACTIONc_scbond_it3.34
X-RAY DIFFRACTIONc_scangle_it54.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 243 5.1 %
Rwork0.33 4503 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.32
X-RAY DIFFRACTIONc_mcbond_it2.392.5
X-RAY DIFFRACTIONc_scbond_it3.34
X-RAY DIFFRACTIONc_mcangle_it3.843
X-RAY DIFFRACTIONc_scangle_it54.5
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rwork: 0.33 / Rfactor obs: 0.33

+
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