[English] 日本語
Yorodumi
- PDB-2jjx: THE CRYSTAL STRUCTURE OF UMP KINASE FROM BACILLUS ANTHRACIS (BA1797) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jjx
TitleTHE CRYSTAL STRUCTURE OF UMP KINASE FROM BACILLUS ANTHRACIS (BA1797)
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PYRIMIDINE BIOSYNTHESIS / ATP-BINDING / URIDYLATE KINASE / NUCLEOTIDE-BINDING / OPPF / PYRH / KINASE / CYTOPLASM / OXFORD PROTEIN PRODUCTION FACILITY (OPPF) / STRUCTURAL PROTEOMICS IN EUROPE (SPINE)
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Uridylate kinase, bacteria / Uridylate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Uridylate kinase / Uridylate kinase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsMeier, C. / Carter, L.G. / Mancini, E.J. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M. / Oxford Protein Production Facility (OPPF) / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Crystal Structure of Ump Kinase from Bacillus Anthracis (Ba1797) Reveals an Allosteric Nucleotide-Binding Site.
Authors: Meier, C. / Carter, L.G. / Sainsbury, S. / Mancini, E.J. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M.
History
DepositionApr 23, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 24, 2017Group: Structure summary
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_asym_id / _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_asym_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5347
Polymers84,9883
Non-polymers1,5464
Water2,558142
1
A: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
hetero molecules

A: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,06814
Polymers169,9766
Non-polymers3,0928
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area19140 Å2
ΔGint-136.3 kcal/mol
Surface area69060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.300, 87.300, 383.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50059, 0.86567, 0.00523), (-0.86568, -0.50056, -0.00554), (-0.00218, -0.0073, 0.99997)82.788, 7.587, -0.43
2given(-0.49555, -0.86822, -0.02504), (0.86843, -0.49579, 0.00392), (-0.01582, -0.01981, 0.99968)49.819, -68.801, 0.222

-
Components

#1: Protein URIDYLATE KINASE / UMP KINASE


Mass: 28329.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: Q81S73, UniProt: A0A6L7HKK4*PLUS, UMP kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 8
Details: 0.2 M LITHIUM SULPHATE, 10% POLYETHYLENE GLYCOL 3000, 0.1 M IMIDAZOLE (PH 8.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.886
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 21872 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 2.82→2.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.6 / % possible all: 98.8

-
Processing

Software
NameClassification
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z9D

1z9d


Resolution: 2.82→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: REGIONS 20-23 AND 171-176 IN EACH CHAIN ARE POORLY ORDERED AND CLASH BETWEEN SYMMETRY RELATED COPIES RESIDUE PHE106 IN A AND B CHAINS CLASH WITH EACH OTHER WHILE RESIDUE PHE106 IN C CHAIN ...Details: REGIONS 20-23 AND 171-176 IN EACH CHAIN ARE POORLY ORDERED AND CLASH BETWEEN SYMMETRY RELATED COPIES RESIDUE PHE106 IN A AND B CHAINS CLASH WITH EACH OTHER WHILE RESIDUE PHE106 IN C CHAIN HAS A SYMMETRY RELATED CLASH WITH ITSELF THE ACTIVE SITE OF EACH CHAIN CONTAINS UNMODELLED ELECTRON DENSITY PRESUMED TO BE ATP WEAKLY BOUND IN THE ABSENCE OF BOUND UMP.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1094 5 %RANDOM
Rwork0.2 ---
obs-21612 --
Refinement stepCycle: LAST / Resolution: 2.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 94 142 5909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

+
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