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- PDB-5vmq: STRUCTURE OF THE R105A MUTANT CATALYTIC TRIMER OF ESCHERICHIA COL... -

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Basic information

Entry
Database: PDB / ID: 5vmq
TitleSTRUCTURE OF THE R105A MUTANT CATALYTIC TRIMER OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE AT 2.0-A RESOLUTION
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / Rossman fold / Mutant / Pyrimidine biosynthesis / Aspartate carbamoyltransferase
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
Aspartate carbamoyltransferase
Similarity search - Component
Biological speciesEscherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.012 Å
AuthorsBeernink, P.T. / Endrizzi, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM019014 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM012159 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM054793 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Charge neutralization in the active site of the catalytic trimer of aspartate transcarbamoylase promotes diverse structural changes.
Authors: Endrizzi, J.A. / Beernink, P.T.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 1GQ3
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8295
Polymers102,7533
Non-polymers762
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-45 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.030, 81.100, 211.650
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: 34250.992 Da / Num. of mol.: 3 / Mutation: R105A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: pyrB, ECS88_4835 / Plasmid: pRCP001 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MLQ3, aspartate carbamoyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM Tris-Cl, 7.5% PEG 8,000, 40 mM CaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→18.29 Å / Num. obs: 57740 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.79 Å2 / Rsym value: 0.071 / Net I/σ(I): 11.7
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.353 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMCCP4data reduction
SCALACCP4data scaling
AMoRECCP4phasing
RefinementResolution: 2.012→18.286 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 22.6 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1998 3.47 %random
Rwork0.1754 ---
obs0.1772 57648 88.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.012→18.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6962 0 2 429 7393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077124
X-RAY DIFFRACTIONf_angle_d0.8399681
X-RAY DIFFRACTIONf_dihedral_angle_d2.8595412
X-RAY DIFFRACTIONf_chiral_restr0.0521129
X-RAY DIFFRACTIONf_plane_restr0.0051255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0116-2.06190.32211270.24063552X-RAY DIFFRACTION81
2.0619-2.11750.27651490.21144124X-RAY DIFFRACTION94
2.1175-2.17980.26171490.18994150X-RAY DIFFRACTION93
2.1798-2.250.26811480.18724116X-RAY DIFFRACTION93
2.25-2.33030.25421480.18514119X-RAY DIFFRACTION93
2.3303-2.42340.21181460.18114086X-RAY DIFFRACTION93
2.4234-2.53340.28071480.17544092X-RAY DIFFRACTION92
2.5334-2.66660.24461460.17814056X-RAY DIFFRACTION91
2.6666-2.83310.23931430.18144018X-RAY DIFFRACTION91
2.8331-3.05090.22421430.1833978X-RAY DIFFRACTION89
3.0509-3.35620.21581420.1743955X-RAY DIFFRACTION88
3.3562-3.83790.21291420.15193919X-RAY DIFFRACTION86
3.8379-4.82070.16991380.14383828X-RAY DIFFRACTION84
4.8207-18.28640.21421290.18893657X-RAY DIFFRACTION77

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