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- PDB-3r7l: Crystal Structure of PALA-bound Aspartate Transcarbamoylase from ... -

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Basic information

Entry
Database: PDB / ID: 3r7l
TitleCrystal Structure of PALA-bound Aspartate Transcarbamoylase from Bacillus subtilis
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Aspartate Transcarbamoylase / PALA / Catalytic Cycle
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/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 / Rossmann fold ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(PHOSPHONACETYL)-L-ASPARTIC ACID / PHOSPHATE ION / Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.585 Å
AuthorsHarris, K.M. / Cockrell, G.M. / Puleo, D.E. / Kantrowitz, E.R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystallographic Snapshots of the Complete Catalytic Cycle of the Unregulated Aspartate Transcarbamoylase from Bacillus subtilis.
Authors: Harris, K.M. / Cockrell, G.M. / Puleo, D.E. / Kantrowitz, E.R.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,32114
Polymers205,6006
Non-polymers1,7218
Water12,971720
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6607
Polymers102,8003
Non-polymers8604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-52 kcal/mol
Surface area31560 Å2
MethodPISA
2
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6607
Polymers102,8003
Non-polymers8604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-54 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.649, 141.432, 114.829
Angle α, β, γ (deg.)90.000, 109.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34266.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: pyrB, BSU15490 / Production host: Escherichia coli (E. coli) / References: UniProt: P05654, aspartate carbamoyltransferase
#2: Chemical
ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10NO8P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 720 / 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: 3.52 Å3/Da / Density % sol: 65.06 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.585→50 Å / Num. obs: 88161 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.126 / Χ2: 1.195 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.585-2.696.80.60887790.9651100
2.69-2.86.90.50987740.9551100
2.8-2.9370.3987761.0021100
2.93-3.087.10.30687971.0481100
3.08-3.287.30.23688091.1251100
3.28-3.537.40.15888051.3031100
3.53-3.887.50.11387961.5071100
3.88-4.457.40.07888141.4361100
4.45-5.67.30.06288521.1941100
5.6-507.70.05689591.3361100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.585→47.275 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7886 / SU ML: 0.35 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 4416 5.02 %
Rwork0.1782 --
obs0.1801 88017 98.91 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.08 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 123.69 Å2 / Biso mean: 36.5865 Å2 / Biso min: 11.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.574 Å20 Å2-1.0998 Å2
2--5.0608 Å20 Å2
3----3.4868 Å2
Refinement stepCycle: LAST / Resolution: 2.585→47.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13752 0 106 720 14578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314048
X-RAY DIFFRACTIONf_angle_d0.73718942
X-RAY DIFFRACTIONf_chiral_restr0.0512154
X-RAY DIFFRACTIONf_plane_restr0.0032454
X-RAY DIFFRACTIONf_dihedral_angle_d13.8395364
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.585-2.67730.27564070.23197656806391
2.6773-2.78440.29134530.227383528805100
2.7844-2.91120.26514680.210284208888100
2.9112-3.06460.27024590.205883868845100
3.0646-3.25660.23864580.193484588916100
3.2566-3.50790.214380.170784228860100
3.5079-3.86080.20044490.167184348883100
3.8608-4.41910.16744200.14584818901100
4.4191-5.56620.18524270.156384788905100
5.5662-47.28330.20084370.18348514895199

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