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- PDB-9y8h: Crystal structure of Ornithine carbamoyltransferase from Burkhold... -

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Basic information

Entry
Database: PDB / ID: 9y8h
TitleCrystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
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 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
Similarity search - Domain/homology
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / PHOSPHATE ION / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesParaburkholderia xenovorans LB400 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionSep 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7687
Polymers38,2111
Non-polymers5566
Water19811
1
A: Ornithine carbamoyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)465,21284
Polymers458,53512
Non-polymers6,67672
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area56770 Å2
ΔGint-435 kcal/mol
Surface area124960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.498, 131.498, 131.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-402-

PO4

21A-402-

PO4

31A-403-

PO4

41A-403-

PO4

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Components

#1: Protein Ornithine carbamoyltransferase / OTCase


Mass: 38211.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia xenovorans LB400 (bacteria)
Gene: argF, Bxe_C0747 / Plasmid: BuxeA.00088.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13H08, ornithine carbamoyltransferase
#2: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: Index G6 : 1.4 M Sodium phosphate monobasic / Potassium phosphate dibasic pH 6.9. BuxeA.00088.a.B2.PW39423 at 24.5 mg/mL. plate 20257 B6 drop 3 , Puck: PSL-0315, Cryo: 4.0 M Sodium phosphate ...Details: Index G6 : 1.4 M Sodium phosphate monobasic / Potassium phosphate dibasic pH 6.9. BuxeA.00088.a.B2.PW39423 at 24.5 mg/mL. plate 20257 B6 drop 3 , Puck: PSL-0315, Cryo: 4.0 M Sodium phosphate monobasic / Potassium phosphate dibasic pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 9, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.67→46.49 Å / Num. obs: 10905 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.041 / Rrim(I) all: 0.186 / Χ2: 1.09 / Net I/σ(I): 19 / Num. measured all: 217846
Reflection shellResolution: 2.67→2.74 Å / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 2.19 / Num. measured all: 16451 / Num. unique obs: 801 / CC1/2: 0.664 / Rpim(I) all: 0.493 / Rrim(I) all: 2.245 / Χ2: 0.96 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5806: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→46.49 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 531 4.87 %
Rwork0.1935 --
obs0.1965 10903 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 29 11 2625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032663
X-RAY DIFFRACTIONf_angle_d0.5183617
X-RAY DIFFRACTIONf_dihedral_angle_d17.219972
X-RAY DIFFRACTIONf_chiral_restr0.039401
X-RAY DIFFRACTIONf_plane_restr0.004468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.940.34831290.28292557X-RAY DIFFRACTION100
2.94-3.360.34271130.22772585X-RAY DIFFRACTION100
3.37-4.240.2441340.1942587X-RAY DIFFRACTION100
4.24-46.490.21581550.16382643X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.3258 Å / Origin y: 0.4391 Å / Origin z: -32.5172 Å
111213212223313233
T0.3328 Å2-0.0022 Å2-0.0571 Å2-0.3357 Å2-0.0011 Å2--0.3119 Å2
L1.1458 °20.2058 °20.2155 °2-1.0208 °20.3161 °2--1.1075 °2
S-0.1632 Å °0.2384 Å °-0.0099 Å °-0.2354 Å °0.0489 Å °0.2131 Å °-0.0972 Å °-0.1208 Å °0.0951 Å °
Refinement TLS groupSelection details: all

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