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

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Basic information

Entry
Database: PDB / ID: 4jhx
TitleCrystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoylphosphate and arginine
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / carbamoylphosphate / L-ornithine
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
ARGININE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / DI(HYDROXYETHYL)ETHER / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsShabalin, I.G. / Bacal, P. / Winsor, J. / Grimshaw, S. / Grabowski, M. / Chordia, M.D. / Shuvalova, L. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structures and kinetic properties of anabolic ornithine carbamoyltransferase from human pathogens Vibrio vulnificus and Bacillus anthracis
Authors: Shabalin, I.G. / Winsor, J. / Grimshaw, S. / Minor, W.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,63111
Polymers118,9263
Non-polymers7058
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-73 kcal/mol
Surface area34530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.029, 79.387, 147.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 334 / Label seq-ID: 27 - 358

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Ornithine carbamoyltransferase / 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 , 5 types, 579 molecules

#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 60 mM Arginine, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 25% w/v PEG ...Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 20 mM Carbamoyl phosphate, 60 mM Arginine, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350, 0.2M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, 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 / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 77488 / Num. obs: 77411 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Χ2: 2.152 / Net I/σ(I): 31.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.85-1.885.80.8632.137990.8630.93699.8
1.88-1.926.40.75638280.98499.9
1.92-1.956.50.62338271.044100
1.95-1.996.60.54538341.119100
1.99-2.046.60.4538271.22299.9
2.04-2.086.70.37938351.316100
2.08-2.146.70.31238061.48599.9
2.14-2.196.70.27438601.62999.9
2.19-2.266.80.23638141.80899.9
2.26-2.336.80.21538751.931100
2.33-2.416.80.18738382.097100
2.41-2.516.80.16738402.261100
2.51-2.636.80.14738872.418100
2.63-2.766.70.12438622.604100
2.76-2.946.70.10338852.83499.9
2.94-3.166.50.08738803.25499.8
3.16-3.486.20.07238953.60899.6
3.48-3.9960.06239203.74999.5
3.99-5.026.10.05339493.57499.5
5.02-5060.04841503.27999.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H31

4h31


Resolution: 1.85→36.61 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1838 / WRfactor Rwork: 0.1477 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8892 / SU B: 5.379 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1324 / SU Rfree: 0.1204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 3848 5 %RANDOM
Rwork0.1541 ---
all0.1559 76761 --
obs0.1559 76638 99.84 %-
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 max: 100.64 Å2 / Biso mean: 32.7125 Å2 / Biso min: 16.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7595 0 39 571 8205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197834
X-RAY DIFFRACTIONr_bond_other_d0.0090.027476
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9510592
X-RAY DIFFRACTIONr_angle_other_deg1.42317156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68125.111360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721534
X-RAY DIFFRACTIONr_chiral_restr0.1140.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029026
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021816
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192200.13
12B192200.13
21A192740.13
22C192740.13
31B194870.11
32C194870.11
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 290 -
Rwork0.201 5319 -
all-5609 -
obs-5319 99.86 %
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)
10.3434-0.12490.02760.4273-0.11290.43-0.0129-0.03890.02130.0546-0.0056-0.0185-0.053-0.00250.01850.0924-0.0135-0.0010.0902-0.01590.0095-6.42917.096-20.003
20.319-0.39090.09790.5482-0.21420.17320.00680.00450.0058-0.0085-0.00520.00950.00430.0156-0.00160.0848-0.00280.00190.0981-0.00660.0358-10.94315.972-29.535
30.1984-0.0446-0.07640.62340.07170.1448-0.02820.0066-0.0180.00890.0019-0.03770.01180.03310.02620.07430.00390.00710.0943-0.00630.02232.273-1.602-29.924
40.7986-0.1091-0.35340.1883-0.01010.3318-0.08-0.1437-0.05570.00230.0548-0.00270.02150.03230.02510.10130.01970.01390.1170.01220.0053-20.8010.42-2.501
51.23260.35280.1361.39480.33190.3064-0.0826-0.2544-0.3092-0.06940.04560.120.11050.07720.03710.18670.04160.04950.11190.09470.1211-37.673-14.4786.121
60.9746-0.05260.2490.6361-0.17550.2004-0.0223-0.05260.0056-0.03080.05510.20330.08170.0585-0.03280.13770.01830.01240.12130.02650.0698-44.16-2.619-0.606
70.44820.00730.08380.4229-0.27220.2759-0.0227-0.04580.02590.04340.040.0413-0.0089-0.0295-0.01730.08940.01910.01050.0906-0.01440.0166-35.97823.073-14.57
80.79990.1679-0.20350.5730.04670.9149-0.01570.0935-0.0025-0.02490.05460.096-0.0259-0.1746-0.03880.0480.0248-0.02850.08950.01040.0621-46.66632.471-34.249
90.3244-0.0514-0.01460.2719-0.00310.1297-0.00260.04140.0031-0.03170.02470.0368-0.03620.0125-0.02210.08810.007-0.01410.0762-00.0404-32.23329.023-36.489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 85
2X-RAY DIFFRACTION2A86 - 149
3X-RAY DIFFRACTION3A150 - 334
4X-RAY DIFFRACTION4B3 - 149
5X-RAY DIFFRACTION5B150 - 248
6X-RAY DIFFRACTION6B249 - 334
7X-RAY DIFFRACTION7C3 - 149
8X-RAY DIFFRACTION8C150 - 253
9X-RAY DIFFRACTION9C254 - 334

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