[English] 日本語
Yorodumi
- PDB-1i5o: CRYSTAL STRUCTURE OF MUTANT R105A OF E. COLI ASPARTATE TRANSCARBA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i5o
TitleCRYSTAL STRUCTURE OF MUTANT R105A OF E. COLI ASPARTATE TRANSCARBAMOYLASE
Components
  • ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
  • ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
KeywordsTRANSFERASE / Mutant aspartate transcarbamoylase / T-state / PALA at the regulatory site
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMacol, C.P. / Tsuruta, H. / Stec, B. / Kantrowitz, E.R.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Direct structural evidence for a concerted allosteric transition in Escherichia coli aspartate transcarbamoylase.
Authors: Macol, C.P. / Tsuruta, H. / Stec, B. / Kantrowitz, E.R.
#1: Journal: Biochemistry / Year: 1990
Title: Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase: Crystal Structures of the Unligated and ATP- and CTP-complexed Enzymes at 2.6-A Resolution.
Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N.
History
DepositionFeb 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1757
Polymers102,7894
Non-polymers3863
Water5,332296
1
A: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,52621
Polymers308,36812
Non-polymers1,1589
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)122.25, 122.25, 142.67
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21C-327-

HOH

31C-331-

HOH

DetailsDeposited data for two catalytic and two regulatory chains Biological assembly: dodecamer can be obtained by application of the threefold crystallographic symmetry

-
Components

#1: Protein ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN / ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN


Mass: 34250.992 Da / Num. of mol.: 2 / Mutation: R105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRB, PYRI / Plasmid: PEK76 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN / ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN


Mass: 17143.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRB, PYRI / Plasmid: PEK76 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10NO8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.7
Details: Tris buffer, maleic acid, pH 5.7, MICRODIALYSIS, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.75 / Details: Jin, L., (2000) Biochemistry, 39, 8058.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlenzyme11
21 mMPALA12
320 mMmaleic acid12
43 mMsodium azide12

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Jul 25, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.78→30 Å / Num. all: 29390 / Num. obs: 29390 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.08 % / Biso Wilson estimate: 26.54 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 5.75
Reflection shellResolution: 2.78→2.99 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1 / Num. unique all: 4622 / % possible all: 75
Reflection
*PLUS
Num. measured all: 90537

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5at1

5at1


Resolution: 2.8→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2172 10 %4 random sets
Rwork0.155 ---
obs0.157 23744 77 %-
all-29390 --
Displacement parametersBiso mean: 31.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7220 0 18 296 7534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_improper_angle_d1.33
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.295 76 10 %
Rwork0.201 821 -
obs-836 62 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.157 / Rfactor obs: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å

+
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