[English] 日本語
Yorodumi
- PDB-2d7j: Crystal Structure Analysis of Glutamine Amidotransferase from Pyr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2d7j
TitleCrystal Structure Analysis of Glutamine Amidotransferase from Pyrococcus horikoshii OT3
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsLIGASE / alpha-beta-alpha
Function / homology
Function and homology information


GMP synthase activity / GMP synthase (glutamine-hydrolysing) / ATP binding / cytosol
Similarity search - Function
GMP synthase (glutamine-hydrolyzing) subunit A / GMP synthase, glutamine amidotransferase / Glutamine amidotransferase / Glutamine amidotransferase class-I / 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
GMP synthase [glutamine-hydrolyzing] subunit A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsMaruoka, S. / Lee, W.C. / Kamo, M. / Kudo, N. / Nagata, K. / Tanokura, M.
CitationJournal: PROC.JPN.ACAD.,SER.B / Year: 2005
Title: Crystal structure of glutamine amidotransferase from Pyrococcus horikoshii OT3
Authors: Maruoka, S. / Lee, W.C. / Kamo, M. / Kudo, N. / Nagata, K. / Tanokura, M.
History
DepositionNov 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GMP synthase [glutamine-hydrolyzing] subunit A


Theoretical massNumber of molelcules
Total (without water)23,7181
Polymers23,7181
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.941, 64.941, 116.408
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

DetailsThis protein works as a monomer.

-
Components

#1: Protein GMP synthase [glutamine-hydrolyzing] subunit A / Class I Glutamine Amidotransferase / Glutamine amidotransferase


Mass: 23718.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: O59071, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2M sodium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.974 Å
DetectorDate: Jun 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 23560
Reflection shellResolution: 1.89→2 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→38.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.174 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21334 1168 5 %RANDOM
Rwork0.1844 ---
all0.18584 ---
obs0.18584 22241 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.268 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 0 53 1550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211531
X-RAY DIFFRACTIONr_bond_other_d0.0020.021416
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.972064
X-RAY DIFFRACTIONr_angle_other_deg1.70333320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021669
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02288
X-RAY DIFFRACTIONr_nbd_refined0.230.2273
X-RAY DIFFRACTIONr_nbd_other0.2510.21522
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0990.2900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.441.5933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.36321511
X-RAY DIFFRACTIONr_scbond_it3.8893598
X-RAY DIFFRACTIONr_scangle_it6.1624.5553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.225 91
Rwork0.177 1617
Refinement TLS params.Method: refined / Origin x: 3.5823 Å / Origin y: 26.5292 Å / Origin z: 10.4578 Å
111213212223313233
T0.0049 Å20.0231 Å2-0.0084 Å2-0.1188 Å2-0.0178 Å2--0.0567 Å2
L3.8157 °2-0.4618 °2-0.652 °2-1.7366 °20.7683 °2--2.6319 °2
S0.0033 Å °0.0265 Å °0.1468 Å °-0.1079 Å °-0.0095 Å °0.0201 Å °-0.0283 Å °0.029 Å °0.0061 Å °

+
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