[English] 日本語
Yorodumi
- PDB-3csu: CATALYTIC TRIMER OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3csu
TitleCATALYTIC TRIMER OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE
ComponentsPROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
KeywordsTRANSFERASE (CARBAMOYL-P / ASPARTATE)
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold ...Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBeernink, P.T. / Endrizzi, J.A. / Alber, T. / Schachman, H.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Assessment of the allosteric mechanism of aspartate transcarbamoylase based on the crystalline structure of the unregulated catalytic subunit.
Authors: Beernink, P.T. / Endrizzi, J.A. / Alber, T. / Schachman, H.K.
History
DepositionApr 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
B: PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
C: PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0915
Polymers103,0113
Non-polymers802
Water14,214789
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-41 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.120, 82.540, 210.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)


Mass: 34337.105 Da / Num. of mol.: 3 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Description: ISOLATED FROM ATCASE HOLOENZYME BY TREATMENT WITH NEOHYDRIN
Gene: PYRB / Plasmid: PAX4 / Gene (production host): PYRB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.37 Å3/Da / Density % sol: 48.01 % / Description: DATA WERE SCANNED WITH 0.15 PIXEL SIZE
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MTris-HCl1reservoir
20.04 M1reservoirCa(OAc)2
37.5 %PEG80001reservoir
46.1 mg/mlprotein1drop
510 mMTris-HCl1drop
61 mM2-mercaptoethanol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→20 Å / Num. obs: 80183 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.4
Reflection shellResolution: 1.88→1.96 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 8ATC

8atc


Resolution: 1.88→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: SER 171 IS MODELED IN TWO CONFORMATIONS THE UNUSUAL B VALUES IN THIS COORDINATE SET ARE DISCUSSED IN THE PAPER CITED ON THE *JRNL* RECORDS ABOVE. BASED ON PRELIMINARY REFINEMENT OF ANOTHER T ...Details: SER 171 IS MODELED IN TWO CONFORMATIONS THE UNUSUAL B VALUES IN THIS COORDINATE SET ARE DISCUSSED IN THE PAPER CITED ON THE *JRNL* RECORDS ABOVE. BASED ON PRELIMINARY REFINEMENT OF ANOTHER T STATE STRUCTURE AGAINST HIGHER RESOLUTION DATA, A MORE TYPICAL B VALUE DISTRIBUTION WAS FOUND. THESE NEW RESULTS WILL BE PUBLISHED WHEN THE REFINEMENT AND ANALYSIS IS COMPLETE.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3971 5 %EVERY 20TH REFLECTION
Rwork0.19 ---
obs-76129 94.6 %-
Solvent computationSolvent model: TNT IMPLEMENTED / Bsol: 290 Å2 / ksol: 0.83 e/Å3
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6809 0 2 789 7600
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00869381.5
X-RAY DIFFRACTIONt_angle_deg1.8593912.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.6541240
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011762
X-RAY DIFFRACTIONt_gen_planes0.01510075
X-RAY DIFFRACTIONt_it1469380
X-RAY DIFFRACTIONt_nbd0.0212910
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.189 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d1.5
X-RAY DIFFRACTIONt_angle_deg2.31.85
X-RAY DIFFRACTIONt_dihedral_angle_d16.65
X-RAY DIFFRACTIONt_planar_d20.01
X-RAY DIFFRACTIONt_plane_restr50.015

+
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