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- PDB-2at2: MOLECULAR STRUCTURE OF BACILLUS SUBTILIS ASPARTATE TRANSCARBAMOYL... -

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Basic information

Entry
Database: PDB / ID: 2at2
TitleMOLECULAR STRUCTURE OF BACILLUS SUBTILIS ASPARTATE TRANSCARBAMOYLASE AT 3.0 ANGSTROMS RESOLUTION
ComponentsASPARTATE CARBAMOYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsStevens, R.C. / Reinisch, K.M. / Lipscomb, W.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Molecular structure of Bacillus subtilis aspartate transcarbamoylase at 3.0 A resolution.
Authors: Stevens, R.C. / Reinisch, K.M. / Lipscomb, W.N.
History
DepositionJul 20, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE CARBAMOYLTRANSFERASE
B: ASPARTATE CARBAMOYLTRANSFERASE
C: ASPARTATE CARBAMOYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)101,3253
Polymers101,3253
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)258.500, 153.200, 51.900
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4987, 0.8667, 0.01248), (-0.8659, -0.4988, 0.03782), (0.039, 0.00805, 0.9921)35.31, 209.83, -3.96
2given(-0.4937, -0.8681, 0.05215), (0.8692, -0.4945, -0.002029), (0.02755, 0.04433, 0.9986)198.85001, 73.82, -6.6
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein ASPARTATE CARBAMOYLTRANSFERASE / Coordinate model: Cα atoms only


Mass: 33775.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / References: UniProt: P05654, aspartate carbamoyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.03 Å3/Da / Density % sol: 75.52 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
21.7 M1drop(NH4)2SO4
30.1 MTris-HCl1drop
42 %PEG2001drop
51.7 M1reservoir(NH4)2SO4
60.1 MTris-HCl1reservoir
1protein solution1drop

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 30228 / % possible obs: 83 % / Num. measured all: 154232 / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Rfactor obs: 0.19 / Highest resolution: 3 Å
Details: BECAUSE OF THE LOW RESOLUTION OF THE STUDY, ONLY CA ATOMS ARE LISTED. RESIDUES 69 - 84, 179 - 191, AND 212 - 229 ARE LOOP REGIONS IN POOR ELECTRON DENSITY AS DISCUSSED IN THE ARTICLE LISTED ...Details: BECAUSE OF THE LOW RESOLUTION OF THE STUDY, ONLY CA ATOMS ARE LISTED. RESIDUES 69 - 84, 179 - 191, AND 212 - 229 ARE LOOP REGIONS IN POOR ELECTRON DENSITY AS DISCUSSED IN THE ARTICLE LISTED ABOVE. THE GEOMETRY OF THESE RESIDUES WERE FIT TO THE SCARCE ELECTRON DENSITY AND ARE NOT NECESSARILY IN OPTIMUM ORIENTATIONS. RESIDUES 296 - 304 ARE NOT LISTED BECAUSE OF A LACK OF ELECTRON DENSITY.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 0 0 885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.028
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 7 Å / Num. reflection obs: 28662 / σ(I): 4 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 4.6

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