[English] 日本語
Yorodumi
- PDB-6kjb: wild-type apo-form E. coli ATCase holoenzyme with an unusual open... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kjb
Titlewild-type apo-form E. coli ATCase holoenzyme with an unusual open conformation of R167
Components
  • Aspartate carbamoyltransferase catalytic subunit
  • Aspartate carbamoyltransferase regulatory chain
KeywordsTRANSFERASE / aspartate transcarbamoylase holoenzyme / de novo pyrimidine biosynthesis
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
Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsWang, N. / Lei, Z. / Zheng, J. / Jia, Z.C.
Funding support China, Canada, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21773014 China
Natural Sciences and Engineering Research Council (Canada)RGPIN-2018-04427 Canada
CitationJournal: Int J Mol Sci / Year: 2020
Title: Conformational Plasticity of the Active Site Entrance inE. coliAspartate Transcarbamoylase and Its Implication in Feedback Regulation.
Authors: Lei, Z. / Wang, N. / Tan, H. / Zheng, J. / Jia, Z.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 3, 2020ID: 4WTO
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5463
Polymers51,4812
Non-polymers651
Water6,395355
1
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)309,27718
Polymers308,88412
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area26160 Å2
ΔGint-86 kcal/mol
Surface area102730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.680, 129.680, 197.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11B-346-

HOH

-
Components

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


Mass: 34337.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pyrB, b4245, JW4204 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pyrI, b4244, JW4203 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7F3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.0 10% Glycerol and 10% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 39940 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.993 / Net I/σ(I): 25.6
Reflection shellResolution: 2.06→2.1 Å / Num. unique obs: 1979 / CC1/2: 0.75

-
Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZA1

1za1


Resolution: 2.06→32.56 Å / Cross valid method: FREE R-VALUE
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2231 3590 5.09 %
Rwork0.1998 --
obs0.2009 39475 91.29 %
Refinement stepCycle: LAST / Resolution: 2.06→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 1 355 3743
LS refinement shellResolution: 2.06→2.08 Å
RfactorNum. reflection% reflection
Rfree0.3072 73 -
Rwork0.266 1449 -
obs--52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27130.0874-0.17090.13810.06540.42180.14490.2081-0.0599-0.16020.1120.09930.0702-0.10580.68510.1932-0.0312-0.10270.1099-0.02560.098-13.700861.69446.1253
20.00710.0067-0.00840.0345-0.02390.02170.0675-0.0333-0.1480.02720.0252-0.02190.1108-0.04830.14790.2163-0.1448-0.18540.17430.02070.2459-15.425241.317817.4972
30.06160.0239-0.0170.06490.03740.04750.04510.024-0.1329-0.05620.0211-0.0536-0.01760.03710.08210.2177-0.0189-0.19860.1433-0.07510.2006-3.095146.858111.6768
40.00130-0.00030.0015-0.00180.00210.0003-0.0022-0.0048-0.004-0.00010.0031-0.0039-0.0036-00.94930.0077-0.07421.02920.01621.0711-62.424371.126621.3199
50.00820.00260.00480.00120.00150.0032-0.01330.0092-0.0155-0.007-0.04510.06370.0002-0.0456-0.00030.3099-0.043-0.0660.6323-0.02751.0679-53.203470.634925.185
60.00460.0038-0.00050.01470.00010-0.02240.0153-0.0361-0.0332-0.0467-0.0261-0.0427-0.04450.00020.4397-0.114-0.08310.6054-0.04550.8437-57.156362.896519.0441
70.0135-0.0012-0.00810.0004-00.0078-0.0124-0.0494-0.06440.04170.04350.15480.021-0.01120.00010.2382-0.05430.01650.22050.08740.3596-32.711660.827222.707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 166 )A1 - 166
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 236 )A167 - 236
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 309 )A237 - 309
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 19 )B11 - 19
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 74 )B20 - 74
6X-RAY DIFFRACTION6chain 'B' and (resid 75 through 101 )B75 - 101
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 153 )B102 - 153

+
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