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- PDB-4kwt: Crystal structure of unliganded anabolic ornithine carbamoyltrans... -

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Basic information

Entry
Database: PDB / ID: 4kwt
TitleCrystal structure of unliganded anabolic ornithine carbamoyltransferase from Vibrio vulnificus at 1.86 A resolution
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Carbamoyl phosphate / ornithine / citrulline / phosphate
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
DI(HYDROXYETHYL)ETHER / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsShabalin, I.G. / Bacal, P. / Bajor, J. / Winsor, J. / Grimshaw, S. / 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
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 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)119,2099
Polymers118,9263
Non-polymers2836
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-20 kcal/mol
Surface area35690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.810, 82.650, 150.908
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: SER / End label comp-ID: SER / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA0 - 33424 - 358
21ALAALABB0 - 33424 - 358
12METMETAA1 - 33425 - 358
22METMETCC1 - 33425 - 358
13METMETBB1 - 33425 - 358
23METMETCC1 - 33425 - 358

NCS ensembles :
ID
1
2
3

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Components

#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
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 60 mM Arginine, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 23% w/v PEG 3350, 0.2M Lithium Sulfate, ...Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 60 mM Arginine, 500 mM NaCl and 5 mM b-mercaptoethanol. Crystallization condition: 0.1M Bis-Tris pH 6.5, 23% w/v PEG 3350, 0.2M Lithium Sulfate, VAPOR DIFFUSION, HANGING 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 [111] / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 82600 / Num. obs: 81196 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Χ2: 2.03 / Net I/σ(I): 35.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.86-1.895.20.9682.140550.9681.00199.2
1.89-1.935.60.82840721.0199.7
1.93-1.965.60.66640421.0499.8
1.96-25.60.55840601.11699.8
2-2.055.60.42940951.15799.7
2.05-2.095.60.35340611.25999.6
2.09-2.155.60.28940651.34699.6
2.15-2.215.60.24140651.47799.5
2.21-2.275.70.20640571.61299.3
2.27-2.345.70.1840591.70999.2
2.34-2.435.70.15440771.91999.1
2.43-2.525.70.13740682.03798.8
2.52-2.645.70.11840482.26898.7
2.64-2.785.70.09940832.43998.5
2.78-2.955.80.08540372.77398
2.95-3.185.70.07240283.21797.4
3.18-3.55.60.06340323.60696.8
3.5-4.015.50.05340293.65796.3
4.01-5.055.60.04340413.07195.5
5.05-505.40.04241222.86792.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4h31


Resolution: 1.86→35.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1949 / WRfactor Rwork: 0.1578 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8569 / SU B: 6.512 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1285 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / 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
Rfree0.1952 4051 5 %RANDOM
Rwork0.1595 ---
all0.1613 82448 --
obs0.1613 81046 98.3 %-
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: 119.35 Å2 / Biso mean: 39.7325 Å2 / Biso min: 19.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å2-0 Å20 Å2
2---0.77 Å2-0 Å2
3---3.62 Å2
Refinement stepCycle: LAST / Resolution: 1.86→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7515 0 11 487 8013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197679
X-RAY DIFFRACTIONr_bond_other_d0.0090.027321
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.94910374
X-RAY DIFFRACTIONr_angle_other_deg1.382316807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21225.313352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.396151319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9631529
X-RAY DIFFRACTIONr_chiral_restr0.1090.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028850
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021763
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A19057
12B19057
21A19093
22C19093
31B19402
32C19402
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 300 -
Rwork0.259 5644 -
all-5944 -
obs-5644 98.61 %
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)
11.4814-0.09620.00010.5153-0.07970.32380.02320.11880.19270.01410.0324-0.06890.0234-0.0572-0.05550.15270.02090.00030.15620.02640.0449-32.94329.97-14.194
21.34761.5217-0.2652.8616-0.2490.0552-0.0803-0.0257-0.1306-0.34680.04610.07120.00620.01590.03420.213-0.0036-0.06520.13650.00980.059-40.62710.619-10.019
31.1926-0.49040.13480.7205-0.04430.790.0680.34250.0495-0.1003-0.0492-0.00870.0031-0.1333-0.01880.15920.02680.00630.24870.04960.0112-42.70531.173-25.438
41.2608-0.18340.02830.67330.20990.78360.05570.54360.1089-0.2101-0.0495-0.0416-0.0479-0.0527-0.00610.20430.03410.01460.38540.07710.0174-38.86233.101-37.126
51.29810.13870.12530.4638-0.07150.9612-0.0363-0.0593-0.0011-0.047-0.02160.03680.02680.01380.05780.1623-0.0026-0.01770.1187-0.00470.0094-21.4836.041-0.347
61.5047-0.1142-0.56310.45310.12670.7641-0.09490.0098-0.0925-0.04370.03410.02790.18890.0120.06090.17860.0013-0.00810.0934-0.00490.0108-20.011-2.099-6.713
72.36890.18350.04331.760.06221.01930.0041-0.1776-0.4182-0.08030.01510.23040.2329-0.0335-0.01930.1811-0.045-0.01660.06340.03960.1141-37.738-11.9995.578
81.66380.32840.09270.8002-0.35170.3249-0.03750.03310.0127-0.14090.08160.19850.11030.0078-0.04410.1591-0.024-0.0390.10940.00310.0963-44.7-0.551-1.853
91.5455-0.2955-0.22030.4538-0.0310.74160.01-0.01530.17420.02990.024-0.12-0.0241-0.0579-0.0340.1144-0.00730.00760.0479-0.01560.0434-5.82919.343-20.892
100.9839-0.6279-0.30820.8711-0.30230.77240.0670.22730.1022-0.0641-0.0411-0.09770.0158-0.1571-0.02590.11380.00080.02660.1360.00330.0231-11.56317.788-30.803
111.23710.0004-0.06381.29260.01350.3304-0.01160.1874-0.0732-0.1489-0.015-0.19810.04390.02990.02660.09240.00690.04560.0862-0.01950.04545.671.101-36.304
120.61560.1551-0.32430.634-0.20670.6065-0.06830.0034-0.04660.1224-0.0093-0.00210.14110.01540.07750.12310.00870.0150.0683-0.01620.0177-2.028-1.852-23.452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 80
2X-RAY DIFFRACTION2A81 - 103
3X-RAY DIFFRACTION3A104 - 192
4X-RAY DIFFRACTION4A193 - 334
5X-RAY DIFFRACTION5B0 - 85
6X-RAY DIFFRACTION6B86 - 149
7X-RAY DIFFRACTION7B150 - 245
8X-RAY DIFFRACTION8B246 - 334
9X-RAY DIFFRACTION9C1 - 80
10X-RAY DIFFRACTION10C81 - 152
11X-RAY DIFFRACTION11C153 - 264
12X-RAY DIFFRACTION12C265 - 334

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