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- PDB-4oh7: Crystal structure of Ornithine carbamoyltransferase from Brucella... -

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Basic information

Entry
Database: PDB / ID: 4oh7
TitleCrystal structure of Ornithine carbamoyltransferase from Brucella melitensis
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / SSGCID / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / 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 speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Ornithine carbamoyltransferase from Brucella melitensis
Authors: Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9458
Polymers70,6262
Non-polymers3196
Water12,809711
1
A: Ornithine carbamoyltransferase
hetero molecules

A: Ornithine carbamoyltransferase
hetero molecules

A: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,41812
Polymers105,9393
Non-polymers4799
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area7620 Å2
ΔGint-34 kcal/mol
Surface area31170 Å2
MethodPISA
2
B: Ornithine carbamoyltransferase
hetero molecules

B: Ornithine carbamoyltransferase
hetero molecules

B: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,41812
Polymers105,9393
Non-polymers4799
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-y+1,x-y+3,z1
crystal symmetry operation3_365-x+y-2,-x+1,z1
Buried area7680 Å2
ΔGint-33 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.450, 88.450, 142.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-798-

HOH

21B-665-

HOH

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Components

#1: Protein Ornithine carbamoyltransferase / OTCase / Ornithine carbamoyltransferase / catabolic


Mass: 35313.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: biotype 2 (strain ATCC 23457) / Gene: arcB, argF, BMEA_A0337 / Plasmid: BrmeB.00183.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0RH19, ornithine carbamoyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BrmeB.00183.a.B1.PS01877 at 20.3 mg/mL, RigakuReagents JCSG+ screen, h8: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5, cryoprotection: 15% ethylene glycol in two steps, ...Details: BrmeB.00183.a.B1.PS01877 at 20.3 mg/mL, RigakuReagents JCSG+ screen, h8: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5, cryoprotection: 15% ethylene glycol in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 100819 / Num. obs: 100352 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 23.829 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.540.392.43208487387199.2
1.54-1.580.3223.54262527241199.9
1.58-1.630.2654.38260897003199.9
1.63-1.680.2255.192554168731100
1.68-1.730.1886.23248426664199.9
1.73-1.790.1517.852386663791100
1.79-1.860.11910.04232056207199.9
1.86-1.940.09712.44222715972199.9
1.94-2.020.07516.03212045719199.9
2.02-2.120.0619.65201415477199.8
2.12-2.240.0522.78187905141199.3
2.24-2.370.04625.29177864911199.4
2.37-2.540.04227.35166614622199.5
2.54-2.740.03729.92153794302199.2
2.74-30.03532.89141023943199.4
3-3.350.03135.56126213552198.7
3.35-3.870.02838.17110503130198.5
3.87-4.740.02640.1496922667199.2
4.74-6.710.02440.2676992076198.9
6.71-500.02339.9238411086192.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL IN DIFFERENT SPACE GROUP OBTAINED FROM IODIDE PHASING

Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1797 / WRfactor Rwork: 0.1519 / FOM work R set: 0.8895 / SU B: 2.42 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0642 / SU Rfree: 0.0666 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 4848 4.8 %RANDOM
Rwork0.1546 ---
all0.1559 100819 --
obs0.1559 100315 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.76 Å2 / Biso mean: 19.044 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 18 711 5285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194843
X-RAY DIFFRACTIONr_bond_other_d0.0010.024669
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9556604
X-RAY DIFFRACTIONr_angle_other_deg0.859310758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10123.971204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07215831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5531533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025554
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021069
X-RAY DIFFRACTIONr_mcbond_it0.8691.0952475
X-RAY DIFFRACTIONr_mcbond_other0.8561.0942474
X-RAY DIFFRACTIONr_mcangle_it1.4091.6383108
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 307 -
Rwork0.222 7073 -
all-7380 -
obs-7073 99.21 %
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)
11.1885-0.602-0.14720.75960.08410.3817-0.0291-0.02950.03950.0761-0.0098-0.0442-0.05680.00810.03890.07770.0029-0.02810.048-0.00330.0127-51.92299.09715.717
21.1568-0.0414-0.0990.4373-0.1820.5678-0.02430.08330.0529-0.0044-0.0051-0.0692-0.06180.08020.02940.0382-0.0185-0.00690.0510.00020.0153-66.975112.117-18.723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 307
2X-RAY DIFFRACTION2B6 - 307

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