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- PDB-6kjb: wild-type apo-form E. coli ATCase holoenzyme with an unusual open... -

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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 / amino acid binding / glutamine metabolic process / 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 / amino acid binding / glutamine metabolic process / 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 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 / 2-Layer 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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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: 2.06→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

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