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- PDB-3sds: Crystal structure of a mitochondrial ornithine carbamoyltransfera... -

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Basic information

Entry
Database: PDB / ID: 3sds
TitleCrystal structure of a mitochondrial ornithine carbamoyltransferase from Coccidioides immitis
ComponentsOrnithine carbamoyltransferase, mitochondrial
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Valley Fever / Coccidioidomycosis / OTCase / mitochondrial / pathogenic fungus / dust-borne pathogen / Carbamoyl phosphate / L-ornithine / L-citrulline / amino acid biosynthesis
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 / mitochondrial matrix
Similarity search - Function
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 ...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, mitochondrial
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsEdwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Expression of proteins in Escherichia coli as fusions with maltose-binding protein to rescue non-expressed targets in a high-throughput protein-expression and purification pipeline.
Authors: Hewitt, S.N. / Choi, R. / Kelley, A. / Crowther, G.J. / Napuli, A.J. / Van Voorhis, W.C.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase, mitochondrial
B: Ornithine carbamoyltransferase, mitochondrial
C: Ornithine carbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2539
Polymers115,0403
Non-polymers2136
Water1,15364
1
A: Ornithine carbamoyltransferase, mitochondrial
hetero molecules

A: Ornithine carbamoyltransferase, mitochondrial
hetero molecules

A: Ornithine carbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2539
Polymers115,0403
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6120 Å2
ΔGint-84 kcal/mol
Surface area35910 Å2
MethodPISA
2
B: Ornithine carbamoyltransferase, mitochondrial
hetero molecules

B: Ornithine carbamoyltransferase, mitochondrial
hetero molecules

B: Ornithine carbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2539
Polymers115,0403
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6780 Å2
ΔGint-125 kcal/mol
Surface area35160 Å2
MethodPISA
3
C: Ornithine carbamoyltransferase, mitochondrial
hetero molecules

C: Ornithine carbamoyltransferase, mitochondrial
hetero molecules

C: Ornithine carbamoyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2539
Polymers115,0403
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5990 Å2
ΔGint-77 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.360, 150.360, 92.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-351-

CL

21C-351-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 349
2114B1 - 349
3114C1 - 349

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Components

#1: Protein Ornithine carbamoyltransferase, mitochondrial / Ornithine transcarbamylase / OTCase


Mass: 38346.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_04084 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL21, ornithine carbamoyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CoimA.01230.a.MB1 PW30353 at 24.3 mg/mL against JCSG+ screen condition B2, 0.2 M PEG 3350, 0.2 M NaSCN with 20% ethylene glycol as cryo-protection reagent, crystal tracking ID 218420b2, pH 7. ...Details: CoimA.01230.a.MB1 PW30353 at 24.3 mg/mL against JCSG+ screen condition B2, 0.2 M PEG 3350, 0.2 M NaSCN with 20% ethylene glycol as cryo-protection reagent, crystal tracking ID 218420b2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 29879 / Num. obs: 29749 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 59.269 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.8-2.8750.6082.66106512141213999.9
2.87-2.950.5393107112158100
2.95-3.040.473.5102012065100
3.04-3.130.3684.410085203499.9
3.13-3.230.2945.539524190899.9
3.23-3.350.2187.449552193799.9
3.35-3.470.1719.2388551794100
3.47-3.610.13112.1988711791100
3.61-3.780.10615.328273167699.9
3.78-3.960.0819.557941160899.8
3.96-4.170.06523.437697155499.8
4.17-4.430.05129.167086145699.9
4.43-4.730.04333.5666831366100
4.73-5.110.03937.596287129299.9
5.11-5.60.04631.765674118399.8
5.6-6.260.04731.1851621090100
6.26-7.230.03637.46439694799.7
7.23-8.850.02155.843976827100
8.85-12.520.01384.16305764699.8
12.520.01478.77120327872.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.79 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.86 Å
Translation3 Å19.86 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1972 / WRfactor Rwork: 0.1628 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8374 / SU B: 29.288 / SU ML: 0.26 / SU R Cruickshank DPI: 3.5844 / SU Rfree: 0.3399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 1504 5.1 %RANDOM
Rwork0.1927 ---
obs0.1951 29661 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.13 Å2 / Biso mean: 55.2221 Å2 / Biso min: 11.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6928 0 6 64 6998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227062
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.959630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3425932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22823.611252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.408151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0311535
X-RAY DIFFRACTIONr_chiral_restr0.0910.21168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215248
X-RAY DIFFRACTIONr_mcbond_it0.4531.54702
X-RAY DIFFRACTIONr_mcangle_it0.85627523
X-RAY DIFFRACTIONr_scbond_it1.12532360
X-RAY DIFFRACTIONr_scangle_it1.8334.52107
Refine LS restraints NCS

Ens-ID: 1 / Number: 2252 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.330.5
2BMEDIUM POSITIONAL0.30.5
3CMEDIUM POSITIONAL0.260.5
1AMEDIUM THERMAL0.452
2BMEDIUM THERMAL0.42
3CMEDIUM THERMAL0.412
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 91 -
Rwork0.255 2019 -
all-2110 -
obs--99.43 %
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)
11.9187-0.344-0.63721.77220.71471.01540.0611-0.14460.10670.1947-0.08740.0962-0.02680.00850.02630.1392-0.01750.01770.0191-0.01690.016866.3136-20.257938.5702
21.1643-0.9904-0.39992.6480.65751.95990.08270.20160.0002-0.1897-0.1782-0.23350.15260.32420.09560.03830.06650.03680.17850.01810.12621.232-13.152322.6836
32.2404-0.85580.1542.4634-0.73561.5182-0.00020.36420.0532-0.2412-0.04270.23130.019-0.39650.0430.05530.0272-0.02680.2718-0.01560.04450.9785-37.7356-8.6195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 349
2X-RAY DIFFRACTION1A350 - 351
3X-RAY DIFFRACTION1A352 - 379
4X-RAY DIFFRACTION2B17 - 349
5X-RAY DIFFRACTION2B350 - 351
6X-RAY DIFFRACTION2B352 - 365
7X-RAY DIFFRACTION3C18 - 349
8X-RAY DIFFRACTION3C350 - 351
9X-RAY DIFFRACTION3C352 - 373

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