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- PDB-6kj7: E. coli ATCase catalytic subunit mutant - G166P -

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Basic information

Entry
Database: PDB / ID: 6kj7
TitleE. coli ATCase catalytic subunit mutant - G166P
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: 2.839 Å
AuthorsLei, Z. / Zheng, J. / Jia, Z.
Funding support China, Canada, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21773014 China
Natural Sciences and Engineering Research Council (NSERC, 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 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)34,3771
Polymers34,3771
Non-polymers00
Water46826
1
A: Aspartate carbamoyltransferase catalytic subunit

A: Aspartate carbamoyltransferase catalytic subunit

A: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)103,1323
Polymers103,1323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4650 Å2
ΔGint-24 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.923, 128.923, 48.253
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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


Mass: 34377.172 Da / Num. of mol.: 1 / Mutation: G166P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pyrB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M NH4Ac, 0.1 M Tris pH 8.5, 20% PEG3350, and 10% glycerol

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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: Jul 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.839→50 Å / Num. obs: 7077 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 44.39 Å2 / CC1/2: 1 / Net I/σ(I): 31.6
Reflection shellResolution: 2.84→2.89 Å / Num. unique obs: 338 / CC1/2: 0.82 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZA1

1za1


Resolution: 2.839→44.293 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 645 9.95 %
Rwork0.2098 5836 -
obs0.2148 6481 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.17 Å2 / Biso mean: 52.1734 Å2 / Biso min: 5.57 Å2
Refinement stepCycle: final / Resolution: 2.839→44.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 0 26 2228
Biso mean---30.1 -
Num. residues----281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.839-3.05810.3409910.262587668
3.0581-3.36580.30781350.2587115091
3.3658-3.85260.29381400.2211267100
3.8526-4.85290.23291400.18411275100
4.8529-44.290.22381390.1908126899
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)
10.05930.0357-0.03570.1890.0420.1165-0.00770.0603-0.001-0.19460.0069-0.2023-0.0451-0.01490.39440.5073-0.01890.13830.42490.30160.476512.456222.63673.9445
20.213-0.09680.02820.5442-0.05520.01070.01420.20590.1446-0.11180.0329-0.0968-0.0502-0.12430.50670.2316-0.0648-0.01260.1850.12820.044210.53758.793812.9739
30.1169-0.00410.01740.0388-0.0190.01020.0720.06410.1621-0.0311-0.06580.0216-0.03770.00370.05240.4495-0.0391-0.00660.22890.20260.4393.041231.877313.3726
40.31930.0260.11410.0148-0.01070.0746-0.0105-0.05330.19270.1315-0.1162-0.1785-0.0049-0.0065-0.00660.4919-0.0570.02540.23460.09280.73257.827436.158819.4219
50.00250.00470.01390.00920.0260.0788-0.0866-0.02150.06980.0424-0.2195-0.0251-0.25760.0293-0.00560.7333-0.18340.0380.4240.02691.16918.575742.250321.5126
60.07750.01980.03540.01280.00340.01990.0514-0.14260.17180.01-0.0527-0.0875-0.0452-0.0653-0.00070.51430.0397-0.00880.2820.03120.6939-7.391237.441219.9294
70.51030.33860.16080.79270.50410.4978-0.0833-0.01120.0906-0.0479-0.2326-0.02620.05250.0933-1.01240.2574-0.04090.02630.25310.21980.3284-3.019123.465612.0289
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 134 )A33 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 166 )A135 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 195 )A167 - 195
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 218 )A196 - 218
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 261 )A219 - 261
7X-RAY DIFFRACTION7chain 'A' and (resid 262 through 308 )A262 - 308

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