[English] 日本語
Yorodumi
- PDB-1oha: Acetylglutamate kinase from Escherichia coli complexed with MgADP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oha
TitleAcetylglutamate kinase from Escherichia coli complexed with MgADP and N-acetyl-L-glutamate
ComponentsACETYLGLUTAMATE KINASE
KeywordsKINASE / N-ACETYL-L-GLUTAMATE KINASE / AMINO ACID KINASE / PHOSPHORYL N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / GROUP TRANSFER / ARGININE METABOLISM
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / phosphorylation / DNA damage response / ATP binding / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, noncyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase / Acetylglutamate kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGil-Ortiz, F. / Ramon-Maiques, S. / Fita, I. / Rubio, V.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Course of Phosphorus in the Reaction of N-Acetyl-L-Glutamate Kinase, Determined from the Structures of Crystalline Complexes, Including a Complex with an Alf(4)(-) Transition State Mimic
Authors: Gil-Ortiz, F. / Ramon-Maiques, S. / Fita, I. / Rubio, V.
History
DepositionMay 23, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8865
Polymers27,1861
Non-polymers7004
Water2,540141
1
A: ACETYLGLUTAMATE KINASE
hetero molecules

A: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,77210
Polymers54,3732
Non-polymers1,3998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)60.126, 71.792, 107.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein ACETYLGLUTAMATE KINASE / / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE


Mass: 27186.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Plasmid: PNAGK24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11445, UniProt: P0A6C8*PLUS, acetylglutamate kinase

-
Non-polymers , 5 types, 145 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 4.6
Details: 27-29% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2K, SODIUM ACETATE 0.1M PH 4.6 AMMONIUM SULFATE 0.15-0.3 M
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127-29 %(w/v)PEG20001reservoir
20.1 Msodium acetate1reservoirpH4.6
30.25-0.4 Mammonium citrate1reservoir
410 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→19.43 Å / Num. obs: 18636 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.3 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19.43 Å / Num. measured all: 154986 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.3

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GS5

1gs5


Resolution: 1.9→19.43 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 944 5.1 %RANDOM
Rwork0.2 ---
obs0.2 18615 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2273 Å2 / ksol: 0.375726 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.35 Å20 Å20 Å2
2--6.91 Å20 Å2
3---0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 45 141 2090
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 186 6.1 %
Rwork0.237 2866 -
obs--99.6 %
Refinement
*PLUS
Num. reflection obs: 17671
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17

+
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