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- PDB-2i6u: Crystal Structure of Ornithine Carbamoyltransferase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2i6u
TitleCrystal Structure of Ornithine Carbamoyltransferase complexed with Carbamoyl Phosphate and L-Norvaline from Mycobacterium tuberculosis (Rv1656) at 2.2 A
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Mycobacterium tuberculosis / ornithine carbamyoltransferase / Carbamoyl phosphate / L-Norvaline / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / 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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / NORVALINE / Ornithine carbamoyltransferase / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSankaranarayanan, R. / Moradian, F. / Cherney, L.T. / Garen, C. / Cherney, M.M. / 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
DepositionAug 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE VAL1 IS IN THE PROTEIN SEQUENCE LISTED AT THE TB CONSORTIUM WEBSITE UNDER THE ACCESSION CODE RV1656.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,44714
Polymers99,1933
Non-polymers1,25511
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-98.3 kcal/mol
Surface area30800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.149, 99.149, 463.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsAssymetric Unit of the crystal contains Trimer which is the Biological entity

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Components

#1: Protein Ornithine carbamoyltransferase / OTCase


Mass: 33064.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: argF, Rv1656, MT1694, MTCY06H11.21 / 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical ChemComp-NVA / NORVALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Magnesium Sulfate, 0.1M Bis-Tris, 8% PEG 400, 3% ethanol, 3mM L-Norvaline, 3mM Carbamoyl phosphate, pH 6.5, 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: Jul 13, 2006
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric 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: 2.2→49.568 Å / Num. all: 69827 / Num. obs: 51538 / % possible obs: 73.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2981 / % possible all: 43.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FB5

1fb5


Resolution: 2.2→49.568 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.93 / SU ML: 0.125 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.28 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23887 2592 5 %RANDOM
Rwork0.17561 ---
obs0.17879 48946 73.81 %-
all-51719 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.994 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å20 Å2
2---1.14 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6978 0 73 572 7623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217163
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9659747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21223.486327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.276151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5481569
X-RAY DIFFRACTIONr_chiral_restr0.1170.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025481
X-RAY DIFFRACTIONr_nbd_refined0.2080.33547
X-RAY DIFFRACTIONr_nbtor_refined0.3120.54857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5937
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.532
X-RAY DIFFRACTIONr_mcbond_it0.8831.54693
X-RAY DIFFRACTIONr_mcangle_it1.527350
X-RAY DIFFRACTIONr_scbond_it2.50332706
X-RAY DIFFRACTIONr_scangle_it4.034.52397
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 115 -
Rwork0.221 2060 -
obs--43.15 %

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