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- PDB-1r0b: Aspartate Transcarbamylase (ATCase) of Escherichia coli: A New Cr... -

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Basic information

Entry
Database: PDB / ID: 1r0b
TitleAspartate Transcarbamylase (ATCase) of Escherichia coli: A New Crystalline R State Bound to PALA, or to Product Analogues Phosphate and Citrate
Components(Aspartate carbamoyltransferase ...) x 2
KeywordsTRANSFERASE / Aspartate Transcarbamylase / Aspartate Carbamoyltransferase / product analogue / citrate / phosphate / ATCase-citrate-phosphate Complex / R state
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
CITRATE ANION / PHOSPHATE ION / Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuang, J. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 2004
Title: Aspartate Transcarbamylase (ATCase) of Escherichia coli: A New Crystalline R-State Bound to PALA, or to Product Analogues Citrate and Phosphate
Authors: Huang, J. / Lipscomb, W.N.
#1: Journal: Proteins / Year: 1999
Title: Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate ...Title: Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1A
Authors: Jin, L. / Stec, B. / Lipscomb, W.N. / Kantrowitz, E.R.
History
DepositionSep 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Aug 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase catalytic chain
C: Aspartate carbamoyltransferase catalytic chain
G: Aspartate carbamoyltransferase regulatory chain
H: Aspartate carbamoyltransferase regulatory chain
I: Aspartate carbamoyltransferase regulatory chain
D: Aspartate carbamoyltransferase catalytic chain
E: Aspartate carbamoyltransferase catalytic chain
F: Aspartate carbamoyltransferase catalytic chain
J: Aspartate carbamoyltransferase regulatory chain
K: Aspartate carbamoyltransferase regulatory chain
L: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,98130
Polymers308,88412
Non-polymers2,09718
Water15,997888
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33620 Å2
ΔGint-168 kcal/mol
Surface area108290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.694, 155.400, 194.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Aspartate carbamoyltransferase ... , 2 types, 12 molecules ABCDEFGHIJKL

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


Mass: 34337.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: PYRB OR B4245 OR C5345 OR Z5856 OR ECS5222 OR SF4245 OR S4507
Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein
Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRI OR B4244 OR C5344 OR Z5855 OR ECS5221 / Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3

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Non-polymers , 4 types, 906 molecules

#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 294 K / Method: microdialysis / pH: 5.8
Details: sodium citrate, sodium phosphate, N-ethylmorpholine, pH 5.8, MICRODIALYSIS, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 12, 2002 / Details: mirrors
RadiationMonochromator: Horizontally bent si(111), assymetrically cut with water coooled Cu block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 81814 / Num. obs: 61088 / % possible obs: 74.7 % / Observed criterion σ(I): -0.9 / Redundancy: 3 % / Biso Wilson estimate: 57.6 Å2 / Rsym value: 0.077 / Net I/σ(I): 13.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 5461 / Rsym value: 0.46 / % possible all: 75.6

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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 1Q95

1q95


Resolution: 2.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 2956 -random
Rwork0.24 ---
all0.26 61065 --
obs0.26 61065 72.5 %-
Displacement parametersBiso mean: 63.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.3 Å20 Å20 Å2
2--14 Å20 Å2
3----27.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1.09 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21696 0 114 888 22698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.62
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.924
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.46 270 -
Rwork0.43 --
obs-5047 62.5 %

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