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

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Basic information

Entry
Database: PDB / ID: 4jqo
TitleCrystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with citrulline and inorganic phosphate
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / carbamoyl phosphate / 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
CITRULLINE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus CMCP6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.082 Å
AuthorsShabalin, I.G. / Winsor, J. / Grimshaw, S. / Domagalski, M.J. / 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 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)120,58519
Polymers118,9263
Non-polymers1,66016
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-49 kcal/mol
Surface area35040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.418, 82.597, 171.968
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: _ / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA-3 - 33321 - 357
21GLNGLNBB-3 - 33321 - 357
12METMETAA1 - 33325 - 357
22METMETCC1 - 33325 - 357
13METMETBB1 - 33325 - 357
23METMETCC1 - 33325 - 357

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 / Fragment: anabolic ornithine carbamoyltransferase, monomer
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus CMCP6 (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, 446 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CIR / CITRULLINE


Type: L-peptide linking / Mass: 175.186 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13N3O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
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, 60 mM L-citrulline, 100 mM NaH2PO4, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 27% w/v PEG 3350, 0. ...Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 60 mM L-citrulline, 100 mM NaH2PO4, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 27% w/v PEG 3350, 0.2M Ammonium sulfate, 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 WAVELENGT / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 69352 / Num. obs: 68312 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Χ2: 2.238 / Net I/σ(I): 21.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.08-2.123.40.678233880.6781.07798.5
2.12-2.153.70.61133511.16999.2
2.15-2.24.10.52234281.20599.5
2.2-2.244.40.49734121.21699.6
2.24-2.294.50.44933901.28499.8
2.29-2.344.50.38733841.31399.6
2.34-2.44.50.34634241.41599.5
2.4-2.474.50.29234351.51399.4
2.47-2.544.50.25534041.62299.4
2.54-2.624.50.22734291.77599.4
2.62-2.714.50.20234162.02399.3
2.71-2.824.50.1834242.27699
2.82-2.954.50.15234002.67199
2.95-3.114.40.12834212.97798.8
3.11-3.34.30.10534393.20898.5
3.3-3.564.20.08433823.44597.7
3.56-3.914.10.0734153.5397.4
3.91-4.484.10.06234143.68296.9
4.48-5.644.20.06234333.71196.9
5.64-503.90.05335233.62993.9

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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
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H31

4h31


Resolution: 2.082→36.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1813 / WRfactor Rwork: 0.1538 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8859 / SU B: 7.371 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1771 / SU Rfree: 0.1448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 3459 5.1 %RANDOM
Rwork0.1616 ---
all0.163 64805 --
obs0.163 68264 97.2 %-
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: 108.09 Å2 / Biso mean: 36.1376 Å2 / Biso min: 19.08 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-0 Å20 Å2
2--0.57 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.082→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 99 430 8297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197997
X-RAY DIFFRACTIONr_bond_other_d0.0080.027619
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.95710780
X-RAY DIFFRACTIONr_angle_other_deg1.277317487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73251009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39325.14358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.398151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.191532
X-RAY DIFFRACTIONr_chiral_restr0.1060.21189
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029178
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021847
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A204400.08
12B204400.08
21A202520.08
22C202520.08
31B204510.06
32C204510.06
LS refinement shellResolution: 2.082→2.136 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 213 -
Rwork0.227 3881 -
all-4094 -
obs--79.98 %
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)
14.9253-6.8337-0.849128.2984-0.21991.5011-0.01970.02980.28690.70420.0308-0.0334-0.1602-0.0873-0.0110.1280.01890.00190.20440.03110.06-16.793-15.83114.695
20.47790.04450.50990.75120.05222.53210.00630.01580.18280.00790.05510.0727-0.07650.0449-0.06140.19710.00840.00480.18450.00290.1077-5.986-17.14815.749
30.65480.20510.05140.5466-0.13010.3423-0.0189-0.02820.0308-0.02290.02040.0350.0086-0.0027-0.00140.1979-0.0002-0.00270.16230.0260.0137-1.559-28.96511.758
40.8842-0.0651-0.12670.3981-0.15980.4028-0.020.00470.1194-0.0054-0.0269-0.0452-0.01110.04060.04680.1919-0.0189-0.00840.15310.03730.032913.852-18.2046.361
56.14681.2233-12.71970.5174-4.979849.1540.02890.31260.11170.2216-0.11310.0113-1.51990.73610.08410.623-0.1370.00440.1997-0.07030.137111.329-29.97854.011
60.69630.02160.0710.662-0.38950.6143-0.0298-0.11290.00950.0529-0.0467-0.0481-0.04760.09590.07660.20550.008-0.0030.24430.02670.010614.715-41.69137.224
72.06850.1641-0.69152.0945-0.142.5222-0.0041-0.2298-0.12010.0991-0.1185-0.55730.02770.49510.12260.12490.056-0.02190.41180.11860.168534.011-53.04943.964
81.1572-0.1166-0.01461.0151-0.17910.81620.0203-0.035-0.2477-0.0869-0.1006-0.06630.10640.11930.08040.23950.06290.03050.24110.05940.072418.665-60.55935.543
97.54-7.2402-5.44089.3-0.044315.788-0.5772-0.2323-0.52620.39750.55090.68160.7624-0.50130.02630.4112-0.16440.05020.24230.12930.175-17.903-60.84633.295
100.8173-0.24720.30990.4937-0.11310.99670.0585-0.0608-0.06830.00470.02620.08690.1888-0.0606-0.08480.2319-0.03820.00010.14830.03820.0275-9.501-54.66824.291
111.02990.4536-0.05161.6886-0.43991.60950.1025-0.0286-0.3752-0.10110.01090.1150.4701-0.1947-0.11350.3217-0.1132-0.08890.11610.01820.1923-20.657-66.2178.728
121.0114-0.0106-0.08850.91770.20921.24320.0680.1395-0.166-0.17640.01230.1110.2159-0.0695-0.08040.2448-0.0467-0.06060.1161-0.0050.0534-15.884-58.8333.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 7
2X-RAY DIFFRACTION2A8 - 39
3X-RAY DIFFRACTION3A40 - 174
4X-RAY DIFFRACTION4A175 - 334
5X-RAY DIFFRACTION5B-5 - 7
6X-RAY DIFFRACTION6B8 - 187
7X-RAY DIFFRACTION7B188 - 225
8X-RAY DIFFRACTION8B226 - 334
9X-RAY DIFFRACTION9C1 - 10
10X-RAY DIFFRACTION10C11 - 149
11X-RAY DIFFRACTION11C150 - 196
12X-RAY DIFFRACTION12C197 - 334

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