[English] 日本語
Yorodumi
- PDB-6kj9: E. coli ATCase catalytic subunit mutant - G128/130A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kj9
TitleE. coli ATCase catalytic subunit mutant - G128/130A
ComponentsAspartate carbamoyltransferase catalytic subunit
KeywordsTRANSFERASE / aspartate transcarbamoylase catalytic subunit / de novo pyrimidine biosynthesis
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate 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
Similarity search - Domain/homology
Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLei, 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: Febs J. / Year: 2020
Title: New regulatory mechanism-based inhibitors of aspartate transcarbamoylase for potential anticancer drug development.
Authors: Lei, Z. / Wang, B. / Lu, Z. / Wang, N. / Tan, H. / Zheng, J. / Jia, Z.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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 catalytic subunit
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase catalytic subunit
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)206,1916
Polymers206,1916
Non-polymers00
Water10,503583
1
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase catalytic subunit
E: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)103,0953
Polymers103,0953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-26 kcal/mol
Surface area34290 Å2
MethodPISA
2
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)103,0953
Polymers103,0953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-26 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.758, 96.729, 121.694
Angle α, β, γ (deg.)90.000, 94.161, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 34365.156 Da / Num. of mol.: 6 / Mutation: G128A, G130A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M NH4Ac, 0.1M Tris pH 8.5, 20% PEG3350, and 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 65582 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.994 / Net I/σ(I): 18.7
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 3280 / CC1/2: 0.784

-
Processing

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

1za1


Resolution: 2.5→48.36 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2283 2005 3.08 %
Rwork0.1916 --
obs0.1928 65143 99.21 %
Refinement stepCycle: LAST / Resolution: 2.5→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13605 0 0 583 14188
LS refinement shellResolution: 2.5→2.56 Å
RfactorNum. reflection% reflection
Rfree0.3183 134 -
Rwork0.2587 4152 -
obs--92 %
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)
10.2153-0.01130.10720.4385-0.15660.2482-0.0876-0.35240.27320.24250.338-0.7833-0.07680.3361-0.01530.4557-0.0084-0.14470.5119-0.09480.47846.91112.6197107.3117
20.18-0.31180.10610.0660.07640.4861-0.0060.13460.10170.18390.1454-0.3269-0.1484-0.18890.0010.41360.0029-0.03960.2735-0.03740.356435.44286.769697.2791
30.31490.02140.02840.5226-0.5370.3654-0.3206-0.55610.099-0.12080.17370.0331-0.0254-0.0287-0.00020.45270.019-0.07030.3834-0.00520.320930.68941.339595.8413
40.8074-0.43050.40051.2433-0.62330.5294-0.0392-0.10580.08680.02050.1175-0.34410.022-0.19580.07050.3436-0.0205-0.09830.3685-0.01180.33439.7156-5.989103.7658
50.3031-0.3913-0.0510.2550.08210.2188-0.3156-0.4065-0.1530.27280.325-0.30130.18180.3545-0.02640.55180.1181-0.17440.5727-0.00090.448642.5126-16.4064119.3567
60.1823-0.19420.310.2387-0.28050.5105-0.6139-0.334-0.54091.10190.54780.0983-0.5041-0.18940.48490.63010.2911-0.18730.75620.16020.14435.9437-14.5163127.4817
70.1734-0.03750.07660.11620.0640.1386-0.58550.2291-0.13310.32330.2450.76770.0814-0.375-0.00980.6574-0.00760.13810.51360.02860.463123.6908-24.7006117.3484
81.1964-0.2402-0.20790.252-0.02450.0857-0.6631-0.2811-0.77770.59220.43620.099-0.3513-0.369-0.34570.65280.3058-0.06370.630.13110.196424.3724-6.9814124.1388
90.4634-0.35350.21570.401-0.36850.1581-0.4272-0.86960.53760.20760.2289-0.2153-0.69910.121-0.11270.5284-0.0118-0.13060.4146-0.11540.451938.26455.8803107.591
100.9561-0.51690.24710.2132-0.34190.8953-0.0168-0.00710.1215-0.2088-0.0318-0.1004-0.1735-0.1679-0.00230.4232-0.01630.0390.2243-0.01140.39630.793615.512773.9641
111.26920.1395-0.6520.8209-0.42110.43910.01550.03040.0464-0.1103-0.0017-0.0334-0.1171-0.072-00.29820.0197-0.00740.2807-0.00410.253620.86877.728477.9069
120.96230.1193-0.35490.9179-0.45141.8138-0.110.1013-0.0124-0.10440.0954-0.02640.1209000.2869-0.00730.09180.21080.00080.390739.6093-0.14957.8936
130.1112-0.25850.00490.21970.00020.06220.2777-0.0921-0.11730.0817-0.2638-0.07990.24-0.25670.00930.4882-0.07620.12830.2239-0.04090.365135.5296-16.218963.0589
140.50870.4323-0.33090.3539-0.04751.315-0.0274-0.1767-0.12790.1839-0.0425-0.10010.12170.206-0.00060.33650.02850.04420.24130.05070.40643.6222-0.135371.5469
152.01990.2683-0.80570.5548-0.57221.496-0.0456-0.15540.00110.1437-0.0748-0.02920.01980.09890.00020.27060.01070.02510.28240.00920.23844.354-38.374105.8921
160.65710.3179-0.31211.9559-0.50221.38910.0594-0.01730.08310.30330.10840.1417-0.059-0.13820.00680.3132-0.00860.07080.34580.00120.2603-9.9776-52.0697118.8308
170.48770.08560.15770.6236-0.51710.4643-0.19890.22070.1643-0.30530.2255-0.178-0.19730.1925-0.00090.2364-0.02410.01830.21960.0230.317419.3479-25.315276.8426
180.50950.39040.36930.58980.58020.44080.0222-0.1818-0.0199-0.1305-0.03080.0532-0.0708-0.06670.00020.21540.01680.00820.2224-0.00060.28768.8739-37.034885.1196
191.08230.15560.30340.21410.31140.87-0.13920.1626-0.0956-0.12970.0632-0.0898-0.10170.063400.23990.0003-0.00630.21930.01090.295821.9653-36.445580.1459
200.5-0.719-0.01950.68180.36260.801-0.16240.251-0.2546-0.20310.3484-0.3957-0.18170.55640.15820.2051-0.09140.02310.3713-0.0170.447241.6618-30.822485.8658
210.46160.1579-0.07020.49830.07720.7799-0.0649-0.2141-0.02880.07190.0614-0.15190.0554-0.0819-0.03690.20580.0186-0.03870.19430.05470.282427.0017-30.503995.0628
220.35260.160.1540.5418-0.25450.4266-0.3923-0.32310.10060.44090.67530.2109-0.6152-0.27640.01950.72930.38180.12310.66820.0440.40397.244921.9887104.7077
230.642-0.3854-0.1040.8515-0.37720.8259-0.1933-0.0809-0.11040.13920.2310.0145-0.3708-0.29050.00680.4170.1386-0.00080.52540.04120.300117.03678.0758101.8504
240.9029-0.6405-0.33090.48220.56080.8175-0.1965-0.5313-0.04840.28850.54490.344-0.0742-0.37260.1610.48290.14860.11630.79970.33460.491-9.840816.442894.3738
25-0.0237-0.3628-0.04281.1542-0.30290.2928-0.2344-0.2006-0.30830.19520.49080.4221-0.1223-0.0861-0.01440.41040.14860.03820.51260.13250.43730.882917.520585.9015
260.74270.52590.19140.8824-0.12911.58250.0772-0.1277-0.00620.0473-0.03390.11010.0082-0.0808-0.00010.24130.0123-0.01530.34640.03980.2907-11.2287-48.885584.4729
270.3380.5951-0.39761.07960.04851.0168-0.0695-0.0311-0.0478-0.30040.1993-0.0030.0511-0.18540.0080.3193-0.0321-0.0890.2777-0.00820.2992-12.5157-60.694160.8624
280.4507-0.0872-0.39050.25590.05640.224-0.03850.0422-0.233-0.41750.13580.02910.16870.09070.00050.4015-0.0077-0.01720.3563-0.05560.32470.7658-62.589258.2128
290.57041.10810.11761.07070.38910.33690.0765-0.06850.0516-0.14670.1963-0.1787-0.13870.05150.00210.25420.0294-0.02480.3211-0.0050.2813-4.4054-47.17568.9064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )A2 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 52 )A33 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 87 )A53 - 87
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 166 )A88 - 166
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 204 )A167 - 204
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 227 )A205 - 227
7X-RAY DIFFRACTION7chain 'A' and (resid 228 through 247 )A228 - 247
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 284 )A248 - 284
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 309 )A285 - 309
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 52 )B1 - 52
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 134 )B53 - 134
12X-RAY DIFFRACTION12chain 'B' and (resid 135 through 223 )B135 - 223
13X-RAY DIFFRACTION13chain 'B' and (resid 224 through 242 )B224 - 242
14X-RAY DIFFRACTION14chain 'B' and (resid 243 through 310 )B243 - 310
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 134 )C1 - 134
16X-RAY DIFFRACTION16chain 'C' and (resid 135 through 309 )C135 - 309
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 32 )D1 - 32
18X-RAY DIFFRACTION18chain 'D' and (resid 33 through 87 )D33 - 87
19X-RAY DIFFRACTION19chain 'D' and (resid 88 through 166 )D88 - 166
20X-RAY DIFFRACTION20chain 'D' and (resid 167 through 227 )D167 - 227
21X-RAY DIFFRACTION21chain 'D' and (resid 228 through 310 )D228 - 310
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 32 )E1 - 32
23X-RAY DIFFRACTION23chain 'E' and (resid 33 through 126 )E33 - 126
24X-RAY DIFFRACTION24chain 'E' and (resid 127 through 223 )E127 - 223
25X-RAY DIFFRACTION25chain 'E' and (resid 224 through 310 )E224 - 310
26X-RAY DIFFRACTION26chain 'F' and (resid 2 through 134 )F2 - 134
27X-RAY DIFFRACTION27chain 'F' and (resid 135 through 221 )F135 - 221
28X-RAY DIFFRACTION28chain 'F' and (resid 222 through 265 )F222 - 265
29X-RAY DIFFRACTION29chain 'F' and (resid 266 through 309 )F266 - 309

+
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