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- PDB-2p2g: Crystal Structure of Ornithine Carbamoyltransferase from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 2p2g
TitleCrystal Structure of Ornithine Carbamoyltransferase from Mycobacterium Tuberculosis (Rv1656): Orthorhombic Form
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Mycobacterium tuberculosis / Ornithine Carbamyoltransferase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function
Ornithine carbamoyltransferase / Ornithine/putrescine 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 ...Ornithine carbamoyltransferase / Ornithine/putrescine 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
Ornithine carbamoyltransferase / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSankaranarayanan, R. / Cherney, M.M. / Cherney, L.T. / Garen, C. / Moradian, F. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and L-norvaline reveal the enzyme's catalytic mechanism.
Authors: Sankaranarayanan, R. / Cherney, M.M. / Cherney, L.T. / Garen, C.R. / Moradian, F. / James, M.N.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,92222
Polymers198,3856
Non-polymers1,53716
Water2,522140
1
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,05712
Polymers99,1933
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-175 kcal/mol
Surface area30530 Å2
MethodPISA, PQS
2
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,86510
Polymers99,1933
Non-polymers6727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-135 kcal/mol
Surface area31080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.166, 144.646, 187.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit of the crystal contains two trimers. Trimer is the biological unit.

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Components

#1: Protein
Ornithine carbamoyltransferase / OTCase


Mass: 33064.195 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: argF, Rv1656, MT1694 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P0A5M8, UniProt: P9WIT9*PLUS, ornithine carbamoyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Magnesium sulfate, 0.1M HEPES pH 7.5, 10% PEG 8000, 3% ETHANOL, Protein concentration 40mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979462 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2006 / Details: Vertical focusing mirror
RadiationMonochromator: Single crystal Si(311) bent (horizontal focusing), Side-scattering cuberoot I-beam bent single crystal, asymmetric cut 12.2 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979462 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 58329 / Num. obs: 58329 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 7.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5375 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1FB5

1fb5


Resolution: 2.7→38.18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.002 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 2.976 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ELECTRON DENSITY FOR THE RESIDUES 227-238 IN THE CHAINS A,B,D,F AND RESIDUES 229-237, 227-232 IN THE CHAINS C AND E, ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ELECTRON DENSITY FOR THE RESIDUES 227-238 IN THE CHAINS A,B,D,F AND RESIDUES 229-237, 227-232 IN THE CHAINS C AND E, RESPECTIVELY, IS WEAK. HENCE, THESE RESIDUES WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25903 2948 5.1 %RANDOM
Rwork0.20172 ---
all0.20468 55313 --
obs0.20468 55313 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.695 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2--0.14 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13487 0 80 140 13707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02113791
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.96118779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91851767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46423.291623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.898152167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3715134
X-RAY DIFFRACTIONr_chiral_restr0.0980.22182
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210510
X-RAY DIFFRACTIONr_nbd_refined0.1910.36228
X-RAY DIFFRACTIONr_nbtor_refined0.3080.59343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5817
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.333
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.510
X-RAY DIFFRACTIONr_mcbond_it0.5291.58996
X-RAY DIFFRACTIONr_mcangle_it0.939214140
X-RAY DIFFRACTIONr_scbond_it1.37335222
X-RAY DIFFRACTIONr_scangle_it2.3144.54639
LS refinement shellResolution: 2.7→2.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 181 -
Rwork0.266 3422 -
obs--82.02 %

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