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- PDB-3e2p: Catalytic subunit of M. Jannaschii aspartate transcarbamoylase in... -

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Basic information

Entry
Database: PDB / ID: 3e2p
TitleCatalytic subunit of M. Jannaschii aspartate transcarbamoylase in an orthorhombic crystal form
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Aspartate Transcarbamoylase / ATCase / pyrimidine biosynthesis / thermostability / Methanococcus jannaschii
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function
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 / Rossmann fold ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVitali, J. / Colaneri, M.J.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form.
Authors: Vitali, J. / Colaneri, M.J.
#1: Journal: PROTEINS / Year: 2008
Title: Crystal structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylas
Authors: Vitali, J. / Colaneri, M.J. / Kantrowitz, E.
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
I: Aspartate carbamoyltransferase
J: Aspartate carbamoyltransferase
K: Aspartate carbamoyltransferase
L: Aspartate carbamoyltransferase
M: Aspartate carbamoyltransferase
N: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,91216
Polymers422,52712
Non-polymers3844
Water9,008500
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7284
Polymers105,6323
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Aspartate carbamoyltransferase
E: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7284
Polymers105,6323
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Aspartate carbamoyltransferase
J: Aspartate carbamoyltransferase
K: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7284
Polymers105,6323
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
L: Aspartate carbamoyltransferase
M: Aspartate carbamoyltransferase
N: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7284
Polymers105,6323
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
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)211,4568
Polymers211,2646
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17290 Å2
ΔGint-21 kcal/mol
Surface area67510 Å2
MethodPISA
6
I: Aspartate carbamoyltransferase
J: Aspartate carbamoyltransferase
K: Aspartate carbamoyltransferase
L: Aspartate carbamoyltransferase
M: Aspartate carbamoyltransferase
N: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,4568
Polymers211,2646
Non-polymers1922
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16920 Å2
ΔGint-22 kcal/mol
Surface area66720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.130, 167.930, 319.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aspartate carbamoyltransferase / Aspartate transcarbamylase / ATCase


Mass: 35210.621 Da / Num. of mol.: 12 / Fragment: catalytic subunit
Source method: isolated from a genetically manipulated source
Details: PSJS1240 was also co-transformed
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: pyrB, MJ1581 / Plasmid: pEK406 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1594 / References: UniProt: Q58976, aspartate carbamoyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.5 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: SI (111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 92280 / % possible obs: 99.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 73.3 Å2 / Rmerge(I) obs: 0.095
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.4 / Num. unique all: 8844 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGW

2rgw


Resolution: 3→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 8653 -random
Rwork0.215 ---
all-92280 --
obs-86643 93.9 %-
Displacement parametersBiso mean: 70 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29602 0 20 500 30122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_dihedral_angle_d21.4

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