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- PDB-1xjw: The Structure of E. coli Aspartate Transcarbamoylase Q137A Mutant... -

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Basic information

Entry
Database: PDB / ID: 1xjw
TitleThe Structure of E. coli Aspartate Transcarbamoylase Q137A Mutant in The R-State
Components
  • Aspartate carbamoyltransferase catalytic chain
  • Aspartate carbamoyltransferase regulatory chain
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / Allosteric enzyme / polar contacts / electrostatics / small angle x-ray scattering / domain closure / intersubunit interactions / TRANSFERASE-TRANSFERASE REGULATOR COMPLEX
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 / Refinement from pre-existing model / Resolution: 2.71 Å
AuthorsStieglitz, K.A. / Alam, N. / Xia, J. / Gourinath, S. / Tsuruta, H. / Kantrowitz, E.R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: A Single Amino Acid Substitution in the Active Site of Escherichia coli Aspartate Transcarbamoylase Prevents the Allosteric Transition.
Authors: Stieglitz, K.A. / Pastra-Landis, S.C. / Xia, J. / Tsuruta, H. / Kantrowitz, E.R.
History
DepositionSep 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 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_asym_id / _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_asym_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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,4888
Polymers102,8474
Non-polymers6414
Water2,090116
1
A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,46524
Polymers308,54212
Non-polymers1,92312
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
Buried area32470 Å2
ΔGint-128 kcal/mol
Surface area105750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.116, 122.116, 155.928
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 34280.059 Da / Num. of mol.: 2 / Mutation: Q137A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrB / Plasmid: pEK 89 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein 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: pyrI / Plasmid: pEK 89 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3
#3: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10NO8P
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.5 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: microdialysis / pH: 5.9
Details: 12 mg/ml Buffer 50 mM Maleic Acid, 3 mM Sodium Azide 1 mM N-Phosphonacetyl-L-Aspartate, pH 5.9, MICRODIALYSIS, temperature 295K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Dec 30, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→7 Å / Num. all: 40234 / Num. obs: 35809 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.0875 / Net I/σ(I): 10.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.59 / Num. unique all: 1380 / % possible all: 85

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
CNSrefinement
SDMSdata scaling
CNSphasing
RefinementMethod to determine structure: Refinement from pre-existing model
Starting model: 1D09

1d09


Resolution: 2.71→7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3580 -RANDOM
Rwork0.17 ---
all0.178 ---
obs0.178 32110 89 %-
Refinement stepCycle: LAST / Resolution: 2.71→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 34 116 7374

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