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- PDB-1f1b: CRYSTAL STRUCTURE OF E. COLI ASPARTATE TRANSCARBAMOYLASE P268A MU... -

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Basic information

Entry
Database: PDB / ID: 1f1b
TitleCRYSTAL STRUCTURE OF E. COLI ASPARTATE TRANSCARBAMOYLASE P268A MUTANT IN THE R-STATE IN THE PRESENCE OF N-PHOSPHONACETYL-L-ASPARTATE
Components
  • ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN
  • ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
KeywordsTRANSFERASE / aspartate transcarbamoylase / aspartate carbamoyltransferase / cis-proline / cis-amino acid
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 / cytosol / cytoplasm
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/ornithine 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/ornithine carbamoyltransferase / 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 / 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 / Resolution: 2.3 Å
AuthorsJin, L. / Stec, B. / Kantrowitz, E.R.
Citation
Journal: Biochemistry / Year: 2000
Title: A cis-proline to alanine mutant of E. coli aspartate transcarbamoylase: kinetic studies and three-dimensional crystal structures.
Authors: Jin, L. / Stec, B. / Kantrowitz, E.R.
#1: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 1999
Title: Insights into the Mechanism of Catalysis and Heterotropic Regulation of Escherichia coli Aspartate Transcarbamoylase based Upon a Structure of the Enzyme Complexed with the Bisubstrate Analog ...Title: Insights into the Mechanism of Catalysis and Heterotropic Regulation of Escherichia coli Aspartate Transcarbamoylase based Upon a Structure of the Enzyme Complexed with the Bisubstrate Analog N-phosphonacetyl-L-aspartate at 2.1 A.
Authors: Jin, L. / Stec, B. / Lipscomb, W.N. / Kantrowitz, E.R.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Nov 3, 2021Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_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_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 2.1Feb 7, 2024Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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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)103,5508
Polymers102,9094
Non-polymers6414
Water18,2311012
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)310,65124
Polymers308,72812
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 area33030 Å2
ΔGint-112 kcal/mol
Surface area103780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.150, 122.150, 156.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1466-

HOH

21A-1556-

HOH

31A-1557-

HOH

41A-1558-

HOH

51C-1531-

HOH

61C-1556-

HOH

71C-1557-

HOH

DetailsThe biological assembly is a dodecamer. The entire molecule requires two symmetry partners generated by rotations around the three-fold

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Components

#1: Protein ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN


Mass: 34311.070 Da / Num. of mol.: 2 / Mutation: P268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Plasmid: PEK412, A PLASMID WITH THE PYRBI GENES INSERTED INTO PUC119
Production host: Escherichia coli (E. coli) / 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)
Plasmid: PEK412, A PLASMID WITH THE PYRBI GENES INSERTED INTO PUC119
Production host: Escherichia coli (E. coli) / 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 / Water


Mass: 18.015 Da / Num. of mol.: 1012 / 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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.75
Details: ENZYME: 7.5 mg/ml in 50 uL microdialysis button. BUFFER: 20 mm maleic acid, 3 mM sodium azide, 1 mM N-phosphonacetyl-L-aspartate, pH 5.75, MICRODIALYSIS, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlenzyme11
21 mMPALA12
320 mMmaleic acid12
43 mMsodium azide12

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Jun 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 60335 / Num. obs: 58790 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.387 / % possible all: 94

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementResolution: 2.3→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 5720 10% random
Rwork0.196 --
obs-57236 -
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 34 1012 8274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_improper_angle_d1.69
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.69

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