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- PDB-4h31: Crystal structure of anabolic ornithine carbamoyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 4h31
TitleCrystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate and L-norvaline
ComponentsOrnithine carbamoyltransferaseOrnithine transcarbamylase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Carbamoyl phosphate and L-ornithine
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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / NORVALINE / DI(HYDROXYETHYL)ETHER / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShabalin, I.G. / Winsor, J. / Grimshaw, S. / Osinski, T. / Chordia, M.D. / Shuvalova, L. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structural studies of ornithine carbamoyltransferase from various pathogens
Authors: Shabalin, I.G. / Winsor, J. / Grimshaw, S. / Osinski, T. / Chordia, M.D. / Anderson, W.F. / Minor, W.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _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
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)123,01936
Polymers118,9263
Non-polymers4,09333
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14160 Å2
ΔGint-48 kcal/mol
Surface area34060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.262, 80.911, 152.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Ornithine carbamoyltransferase / Ornithine transcarbamylase / OTCase


Mass: 39641.938 Da / Num. of mol.: 3
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 / References: UniProt: Q8DCF5, ornithine carbamoyltransferase

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Non-polymers , 6 types, 528 molecules

#2: Chemical ChemComp-NVA / NORVALINE / Norvaline


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Carbamoyl phosphate


Mass: 141.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 20 mM L-norvaline, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.2 M Ammonium Acetate, 0.1 M Bis- ...Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 20 mM L-norvaline, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.2 M Ammonium Acetate, 0.1 M Bis-Tris pH 5.5, 23% PEG 3350, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2012 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 102701 / Num. obs: 102659 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 29.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5067 / Rsym value: 0.963 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.6.0117refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPD

3upd


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.116 / SU ML: 0.052 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16735 5088 5 %RANDOM
Rwork0.13541 ---
all0.13704 96750 --
obs0.13704 96702 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.753 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---0.04 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7712 0 206 495 8413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198146
X-RAY DIFFRACTIONr_bond_other_d0.0010.025501
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.96610967
X-RAY DIFFRACTIONr_angle_other_deg1.049313487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71851036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63125.353368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.539151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.341532
X-RAY DIFFRACTIONr_chiral_restr0.1120.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021600
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 364 -
Rwork0.196 6677 -
obs--99.99 %
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)
10.6945-0.2262-0.07590.42120.0380.38150.0207-0.03490.06080.0433-0.0097-0.0255-0.02910.0239-0.0110.1556-0.00650.01060.0652-0.00360.0676-7.85614.71-25.038
20.4804-0.0605-0.18010.80950.15430.4298-0.01970.0107-0.0283-0.0082-0.0016-0.05350.03150.04230.02130.13540.00990.00820.06570.00490.06152.742-3.462-31.848
30.58390.1509-0.23510.4807-0.25370.5909-0.0024-0.116-0.01690.0603-0.0362-0.0321-0.00260.04140.03860.1712-0.00840.00660.09010.01330.0373-19.398-2.013-3.649
41.05690.3532-0.00631.0604-0.34240.53930.001-0.1006-0.078-0.02450.06730.12630.0662-0.0845-0.06830.1808-0.02130.01310.10710.03670.0507-39.058-11.924-0.473
50.44990.07650.14260.8435-0.38360.71920.0208-0.08160.04260.13420.05080.128-0.0872-0.0768-0.07150.17740.0190.04370.0805-0.00380.0803-34.72620.645-14.286
60.6462-0.08360.17811.2342-0.08770.8494-0.00020.04510.0403-0.1190.03690.2525-0.0699-0.0773-0.03670.10570.0118-0.00880.01490.01650.0675-39.93228.006-34.402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 150
2X-RAY DIFFRACTION2A151 - 333
3X-RAY DIFFRACTION3B1 - 150
4X-RAY DIFFRACTION4B151 - 333
5X-RAY DIFFRACTION5C1 - 150
6X-RAY DIFFRACTION6C151 - 334

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