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- PDB-3csu: CATALYTIC TRIMER OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE -

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Basic information

Entry
Database: PDB / ID: 3csu
TitleCATALYTIC TRIMER OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE
ComponentsPROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
KeywordsTRANSFERASE (CARBAMOYL-P / ASPARTATE)
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / cytosol / cytoplasm
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
Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBeernink, P.T. / Endrizzi, J.A. / Alber, T. / Schachman, H.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Assessment of the allosteric mechanism of aspartate transcarbamoylase based on the crystalline structure of the unregulated catalytic subunit.
Authors: Beernink, P.T. / Endrizzi, J.A. / Alber, T. / Schachman, H.K.
History
DepositionApr 22, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
B: PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
C: PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0915
Polymers103,0113
Non-polymers802
Water14,214789
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-41 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.120, 82.540, 210.520
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 PROTEIN (ASPARTATE CARBAMOYLTRANSFERASE)


Mass: 34337.105 Da / Num. of mol.: 3 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Description: ISOLATED FROM ATCASE HOLOENZYME BY TREATMENT WITH NEOHYDRIN
Gene: PYRB / Plasmid: PAX4 / Gene (production host): PYRB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.37 Å3/Da / Density % sol: 48.01 % / Description: DATA WERE SCANNED WITH 0.15 PIXEL SIZE
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MTris-HCl1reservoir
20.04 M1reservoirCa(OAc)2
37.5 %PEG80001reservoir
46.1 mg/mlprotein1drop
510 mMTris-HCl1drop
61 mM2-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→20 Å / Num. obs: 80183 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.4
Reflection shellResolution: 1.88→1.96 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 8ATC

8atc


Resolution: 1.88→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: SER 171 IS MODELED IN TWO CONFORMATIONS THE UNUSUAL B VALUES IN THIS COORDINATE SET ARE DISCUSSED IN THE PAPER CITED ON THE *JRNL* RECORDS ABOVE. BASED ON PRELIMINARY REFINEMENT OF ANOTHER T ...Details: SER 171 IS MODELED IN TWO CONFORMATIONS THE UNUSUAL B VALUES IN THIS COORDINATE SET ARE DISCUSSED IN THE PAPER CITED ON THE *JRNL* RECORDS ABOVE. BASED ON PRELIMINARY REFINEMENT OF ANOTHER T STATE STRUCTURE AGAINST HIGHER RESOLUTION DATA, A MORE TYPICAL B VALUE DISTRIBUTION WAS FOUND. THESE NEW RESULTS WILL BE PUBLISHED WHEN THE REFINEMENT AND ANALYSIS IS COMPLETE.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3971 5 %EVERY 20TH REFLECTION
Rwork0.19 ---
obs-76129 94.6 %-
Solvent computationSolvent model: TNT IMPLEMENTED / Bsol: 290 Å2 / ksol: 0.83 e/Å3
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6809 0 2 789 7600
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00869381.5
X-RAY DIFFRACTIONt_angle_deg1.8593912.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.6541240
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011762
X-RAY DIFFRACTIONt_gen_planes0.01510075
X-RAY DIFFRACTIONt_it1469380
X-RAY DIFFRACTIONt_nbd0.0212910
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.189 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d1.5
X-RAY DIFFRACTIONt_angle_deg2.31.85
X-RAY DIFFRACTIONt_dihedral_angle_d16.65
X-RAY DIFFRACTIONt_planar_d20.01
X-RAY DIFFRACTIONt_plane_restr50.015

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