[English] 日本語
Yorodumi
- PDB-1b7b: Carbamate kinase from Enterococcus faecalis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b7b
TitleCarbamate kinase from Enterococcus faecalis
ComponentsCARBAMATE KINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / ARGININE CATABOLISM / ATP SYNTHESYS / ACYLPHOSPHATE-MAKING ENZYMES / OPEN ALPHA/BETA SHEET
Function / homology
Function and homology information


: / carbamate kinase / carbamate kinase activity / arginine metabolic process / ATP binding / cytoplasm
Similarity search - Function
Carbamate kinase / 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
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsMarina, A. / Alzari, P.M. / Bravo, J. / Uriarte, M. / Barcelona, B. / Fita, I. / Rubio, V.
CitationJournal: Protein Sci. / Year: 1999
Title: Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine.
Authors: Marina, A. / Alzari, P.M. / Bravo, J. / Uriarte, M. / Barcelona, B. / Fita, I. / Rubio, V.
History
DepositionJan 20, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: CARBAMATE KINASE
B: CARBAMATE KINASE
C: CARBAMATE KINASE
D: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2198
Polymers131,8344
Non-polymers3844
Water1,22568
1
A: CARBAMATE KINASE
C: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1094
Polymers65,9172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-57 kcal/mol
Surface area25480 Å2
MethodPISA
2
B: CARBAMATE KINASE
D: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1094
Polymers65,9172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-57 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.860, 172.920, 98.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999953, 0.009657, -0.001168), (0.008817, 0.849089, -0.528177), (-0.004109, -0.528162, -0.849134)28.049, 13.1245, 46.2127
2given(-0.997496, -0.043989, -0.055375), (-0.011779, 0.875414, -0.483231), (0.069733, -0.481369, -0.87374)33.4157, 47.7554, 81.4565
3given(0.997176, 0.03716, 0.065267), (-0.040201, 0.998136, 0.045918), (-0.063439, -0.048412, 0.996811)-5.6123, 11.0275, -48.0873

-
Components

#1: Protein
CARBAMATE KINASE / / EC 2.7.2.2


Mass: 32958.578 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: COMPLEXED WITH SULPHATE ANION / Source: (natural) Enterococcus faecium (bacteria) / Cellular location: CYTOPLASM / Plasmid: PCK41 / Strain: D10 / References: UniProt: P0A2X8, carbamate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.62 Å3/Da / Density % sol: 52.62 %
Crystal growpH: 6.4 / Details: PEG 4000, (NH4)2SO4, SODIUM CACODYLATE, pH 6.4
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2(NH4)2SO411
3sodium CACODylate11
Crystal grow
*PLUS
Method: other / Details: Marina, A., (1994) J. Mol. Biol., 235, 1345.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 31935 / % possible obs: 89.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→15 Å / Data cutoff low absF: 200 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2893 10.2 %RANDOM
Rwork0.224 ---
obs-28366 89.5 %-
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9424 0 20 68 9512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 0 Å2 / Rms dev position: 0 Å / Weight Biso : 2 / Weight position: 30

Ens-IDDom-IDNCS model details
11RESTRAINTS
22
33
44
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.344 279 11 %
Rwork0.287 2531 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10.2 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.344 / % reflection Rfree: 11 % / Rfactor Rwork: 0.287

+
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