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- PDB-1i5o: CRYSTAL STRUCTURE OF MUTANT R105A OF E. COLI ASPARTATE TRANSCARBA... -

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Basic information

Entry
Database: PDB / ID: 1i5o
TitleCRYSTAL STRUCTURE OF MUTANT R105A OF E. COLI ASPARTATE TRANSCARBAMOYLASE
Components
  • ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
  • ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
KeywordsTRANSFERASE / Mutant aspartate transcarbamoylase / T-state / PALA at the regulatory site
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMacol, C.P. / Tsuruta, H. / Stec, B. / Kantrowitz, E.R.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Direct structural evidence for a concerted allosteric transition in Escherichia coli aspartate transcarbamoylase.
Authors: Macol, C.P. / Tsuruta, H. / Stec, B. / Kantrowitz, E.R.
#1: Journal: Biochemistry / Year: 1990
Title: Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase: Crystal Structures of the Unligated and ATP- and CTP-complexed Enzymes at 2.6-A Resolution.
Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N.
History
DepositionFeb 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_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 1.4Aug 9, 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 TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1757
Polymers102,7894
Non-polymers3863
Water5,332296
1
A: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
B: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
C: ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN
D: ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,52621
Polymers308,36812
Non-polymers1,1589
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
Unit cell
Length a, b, c (Å)122.25, 122.25, 142.67
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-322-

HOH

21C-327-

HOH

31C-331-

HOH

DetailsDeposited data for two catalytic and two regulatory chains Biological assembly: dodecamer can be obtained by application of the threefold crystallographic symmetry

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Components

#1: Protein ASPARTATE TRANSCARBAMOYLASE CATALYTIC CHAIN / ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN


Mass: 34250.992 Da / Num. of mol.: 2 / Mutation: R105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRB, PYRI / Plasmid: PEK76 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein ASPARTATE TRANSCARBAMOYLASE REGULATORY CHAIN / 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: PYRB, PYRI / Plasmid: PEK76 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10NO8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.7
Details: Tris buffer, maleic acid, pH 5.7, MICRODIALYSIS, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.75 / Details: Jin, L., (2000) Biochemistry, 39, 8058.
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 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Jul 25, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.78→30 Å / Num. all: 29390 / Num. obs: 29390 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.08 % / Biso Wilson estimate: 26.54 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 5.75
Reflection shellResolution: 2.78→2.99 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1 / Num. unique all: 4622 / % possible all: 75
Reflection
*PLUS
Num. measured all: 90537

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5at1

5at1


Resolution: 2.8→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2172 10 %4 random sets
Rwork0.155 ---
obs0.157 23744 77 %-
all-29390 --
Displacement parametersBiso mean: 31.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7220 0 18 296 7534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.95
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_improper_angle_d1.33
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.295 76 10 %
Rwork0.201 821 -
obs-836 62 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.157 / Rfactor obs: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å

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