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- PDB-3upd: 2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 3upd
Title2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus
ComponentsOrnithine carbamoyltransferaseOrnithine transcarbamylase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha and beta proteins (a/b) / ATC-like / Aspartate/ornithine carbamoyltransferase
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / 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
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.9 Angstrom Crystal Structure of Ornithine Carbamoyltransferase (ArgF) from Vibrio vulnificus.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)39,6421
Polymers39,6421
Non-polymers00
Water84747
1
A: Ornithine carbamoyltransferase

A: Ornithine carbamoyltransferase

A: Ornithine carbamoyltransferase


Theoretical massNumber of molelcules
Total (without water)118,9263
Polymers118,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area6510 Å2
ΔGint-15 kcal/mol
Surface area40320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.963, 153.963, 153.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Ornithine carbamoyltransferase / Ornithine transcarbamylase / OTCase


Mass: 39641.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: argF, VV1_1466 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q8DCF5, ornithine carbamoyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 7.2mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: Calssics II (C2), 1.1M Ammonium tartrate (pH 7.0); Cryo: 4.0M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 13533 / Num. obs: 13533 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 82.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.3 / Num. unique all: 642 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DUV

1duv


Resolution: 2.91→28.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 23.258 / SU ML: 0.191
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19452 669 4.9 %RANDOM
Rwork0.15799 ---
all0.15978 12861 --
obs0.15978 12861 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.788 Å2
Refinement stepCycle: LAST / Resolution: 2.91→28.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 0 47 2745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222753
X-RAY DIFFRACTIONr_bond_other_d0.0010.021834
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9383715
X-RAY DIFFRACTIONr_angle_other_deg0.88534479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8985344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.98125132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73115475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6371511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_mcbond_it0.8821.51709
X-RAY DIFFRACTIONr_mcbond_other0.1531.5711
X-RAY DIFFRACTIONr_mcangle_it1.73122728
X-RAY DIFFRACTIONr_scbond_it2.74731044
X-RAY DIFFRACTIONr_scangle_it4.3764.5987
LS refinement shellResolution: 2.905→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 54 -
Rwork0.264 917 -
obs-917 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.888812.5791.957532.49485.962712.73420.3766-0.20650.82691.2944-0.44561.86380.67220.59380.06891.42720.2947-0.2260.9319-0.32021.388524.5251-0.323932.9364
20.87980.3111-0.1021.8405-0.39931.08140.01020.17870.0082-0.18980.03930.06260.024-0.1465-0.04950.04450.01370.00250.09870.00020.008221.0386-22.041630.7513
34.72951.0081-0.71790.88720.22833.1969-0.15220.6074-0.2804-0.51820.1581-0.13610.21110.0211-0.00590.4306-0.02830.06350.197-0.0440.025532.1102-18.03710.9466
41.0318-0.3516-0.30010.9763-0.39032.37510.03950.14920.0501-0.2206-0.1185-0.2249-0.06990.31450.0790.1266-0.02140.08740.09810.01070.071640.0707-13.825823.2839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-22 - -17
2X-RAY DIFFRACTION2A-5 - 183
3X-RAY DIFFRACTION3A184 - 249
4X-RAY DIFFRACTION4A250 - 334

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