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- PDB-2air: T-state Active Site of Aspartate Transcarbamylase:Crystal Structu... -

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Basic information

Entry
Database: PDB / ID: 2air
TitleT-state Active Site of Aspartate Transcarbamylase:Crystal Structure of the Carbamyl Phosphate and L-alanosine Ligated Enzyme
Components(Aspartate carbamoyltransferase ...) x 2
KeywordsTRANSFERASE / Aspartate Transcarbamylase / Alanosine / Carbamyl Phosphate / T-state
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / pyrimidine nucleotide biosynthetic process / amino acid binding / cellular amino acid metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding ...aspartate carbamoyltransferase complex / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / pyrimidine nucleotide biosynthetic process / amino acid binding / cellular amino acid metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytosol / cytoplasm
Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate and ornithine carbamoyltransferases signature. / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily ...Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate and ornithine carbamoyltransferases signature. / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase / Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain
Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, J. / Lipscomb, W.N.
CitationJournal: Biochemistry / Year: 2006
Title: T-State Active Site of Aspartate Transcarbamylase: Crystal Structure of the Carbamyl Phosphate and l-Alanosine Ligated Enzyme
Authors: Huang, J. / Lipscomb, W.N.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 21, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id

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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
G: Aspartate carbamoyltransferase catalytic chain
H: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,67310
Polymers102,9614
Non-polymers7116
Water10,917606
1
A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
G: Aspartate carbamoyltransferase catalytic chain
H: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
G: Aspartate carbamoyltransferase catalytic chain
H: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
G: Aspartate carbamoyltransferase catalytic chain
H: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,01830
Polymers308,88412
Non-polymers2,13318
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 area32630 Å2
ΔGint-136 kcal/mol
Surface area112660 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)129.152, 129.152, 198.097
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-873-

HOH

21A-881-

HOH

31B-837-

HOH

41G-891-

HOH

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Components

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Aspartate carbamoyltransferase ... , 2 types, 4 molecules AGBH

#1: Protein/peptide Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase


Mass: 34337.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrB / Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein/peptide 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: pyrI / Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3

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Non-polymers , 4 types, 612 molecules

#3: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical ChemComp-AL0 / 3-[HYDROXY(NITROSO)AMINO]-L-ALANINE / L-ALANOSINE


Mass: 149.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N3O4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-4000, iso-propranol, sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 9, 2004 / Details: mirrors
RadiationMonochromator: Horizontally bent si (111), assymetrically cut with water cooled Cu block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 130959 / Num. obs: 74502 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 0.71 / Num. unique all: 2377 / % possible all: 56.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D09
Resolution: 2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3363 -random
Rwork0.239 ---
All0.239 69425 --
Obs0.239 65707 78.9 %-
Displacement parametersBiso mean: 57.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.706 Å2-3.988 Å2-
2---0.7 Å2-
3---1.413 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7232 0 38 606 7876
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_d1.49
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.4032 212 -
Rwork0.4167 --
Obs-4069 48.8 %

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