[English] 日本語
Yorodumi
- PDB-1q95: Aspartate Transcarbamylase (ATCase) of Escherichia coli: A New Cr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q95
TitleAspartate Transcarbamylase (ATCase) of Escherichia coli: A New Crystalline R State Bound to PALA, or to Product Analogues Phosphate and Citrate
Components
  • Aspartate carbamoyltransferase catalytic chain
  • Aspartate carbamoyltransferase regulatory chain
KeywordsTRANSFERASE / Aspartate Transcarbamylase / Aspartate Carbamoyltransferase / N-carbamyl-L-aspartate / PALA / ATCase-PALA Complex / R state
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / 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 / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
N-(PHOSPHONACETYL)-L-ASPARTIC ACID / Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsHuang, J. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 2004
Title: Aspartate Transcarbamylase (ATCase) of Escherichia coli: A New Crystalline R-State Bound to PALA, or to Product Analogues Citrate and Phosphate
Authors: Huang, J. / Lipscomb, W.N.
#1: Journal: Proteins / Year: 1999
Title: Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate ...Title: Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1A
Authors: Jin, L. / Stec, B. / Lipscomb, W.N. / Kantrowitz, E.R.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase catalytic chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase catalytic chain
E: Aspartate carbamoyltransferase catalytic chain
F: Aspartate carbamoyltransferase catalytic chain
G: Aspartate carbamoyltransferase regulatory chain
H: Aspartate carbamoyltransferase regulatory chain
I: Aspartate carbamoyltransferase regulatory chain
J: Aspartate carbamoyltransferase regulatory chain
K: Aspartate carbamoyltransferase regulatory chain
L: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,80824
Polymers308,88412
Non-polymers1,92312
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31490 Å2
ΔGint-126 kcal/mol
Surface area109170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.510, 153.490, 185.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase


Mass: 34337.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: PYRB OR B4245 OR C5345 OR Z5856 OR ECS5222 OR SF4245 OR S4507
Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein
Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRI OR B4244 OR C5344 OR Z5855 OR ECS5221 / Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3
#3: Chemical
ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10NO8P
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG-mmes 2000, lithium sulfate, sodium azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2001 / Details: mirrors
RadiationMonochromator: Horizontally bent si(111), assymetrically cut with water coooled Cu block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. all: 147443 / Num. obs: 113497 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.5 / Redundancy: 1.3 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 13.1
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 9571 / Rsym value: 0.41 / % possible all: 74.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D09

1d09


Resolution: 2.46→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5388 -random
Rwork0.23 ---
all0.24 126367 --
obs0.24 106993 84.7 %-
Displacement parametersBiso mean: 63.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.833 Å20 Å20 Å2
2---9.074 Å20 Å2
3---8.241 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.46→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21696 0 102 822 22620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.42
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.785
LS refinement shellResolution: 2.46→2.55 Å
RfactorNum. reflection% reflection
Rfree0.386 431 -
Rwork0.368 --
obs-7881 62.9 %

+
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