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- PDB-7tmd: Crystal structure of Ornithine carbamoyltransferase from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 7tmd
TitleCrystal structure of Ornithine carbamoyltransferase from Klebsiella pneumoniae
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / Ornithine carbamoyltransferase / 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 / 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
BROMIDE ION / IODIDE ION / ornithine carbamoyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal structure of Ornithine carbamoyltransferase from Klebsiella pneumoniae
Authors: Lovell, S. / Liu, L. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,7549
Polymers225,4676
Non-polymers2873
Water9,080504
1
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9405
Polymers112,7333
Non-polymers2072
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-25 kcal/mol
Surface area35630 Å2
MethodPISA
2
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8134
Polymers112,7333
Non-polymers801
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-25 kcal/mol
Surface area34730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.093, 154.714, 150.557
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-401-

IOD

21A-592-

HOH

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Components

#1: Protein
Ornithine carbamoyltransferase


Mass: 37577.824 Da / Num. of mol.: 6 / Fragment: KlpnC.00088.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_05120 / Plasmid: KlpnC.00088.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GHJ1, ornithine carbamoyltransferase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.91 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus B10: 12% (v/v) Ethylene glycol: 6 % (w/v) PEG 8000, 0.1 M (Sodium HEPES: MOPS (acid)), 0.03M Sodium fluoride: 0.03M Sodium bromide: 0.03M Sodium iodide: KlpnC.00088.a.B1.PS38685 at ...Details: Morpheus B10: 12% (v/v) Ethylene glycol: 6 % (w/v) PEG 8000, 0.1 M (Sodium HEPES: MOPS (acid)), 0.03M Sodium fluoride: 0.03M Sodium bromide: 0.03M Sodium iodide: KlpnC.00088.a.B1.PS38685 at 24.8 mg/mL, Tray: plate 12314 well B10 drop 1, Puck: PSL1108, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→48.79 Å / Num. obs: 88612 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.4 / Num. measured all: 312992 / Scaling rejects: 343
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.35-2.393.60.5441650545690.7872.598.9
12.66-48.793.50.05421266000.98516.298.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.20_4474refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DUV

1duv


Resolution: 2.35→47.54 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 4410 4.98 %
Rwork0.1713 84119 -
obs0.1747 88529 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.81 Å2 / Biso mean: 35.0523 Å2 / Biso min: 12.92 Å2
Refinement stepCycle: final / Resolution: 2.35→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15037 0 5 504 15546
Biso mean--33.02 33.19 -
Num. residues----1978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.380.29741590.21692818297799
2.38-2.40.30061620.22442789295199
2.4-2.430.36031210.22432860298199
2.43-2.460.28781090.2152841295099
2.46-2.50.30481490.20552827297699
2.5-2.530.23731420.20342789293199
2.53-2.570.28091600.19682814297499
2.57-2.610.26981690.2032795296499
2.61-2.650.2911670.19872801296898
2.65-2.690.27421320.1972795292798
2.69-2.740.3041400.20072816295698
2.74-2.790.33211230.20522696281994
2.79-2.840.25561270.20242600272791
2.84-2.90.24351310.20012865299699
2.9-2.960.28671340.20012846298099
2.96-3.030.27661620.19132820298299
3.03-3.110.27482110.18452760297199
3.11-3.190.27221710.17712806297799
3.19-3.280.26241580.18332848300699
3.28-3.390.28841750.18982802297799
3.39-3.510.23321380.16962847298599
3.51-3.650.23541520.16172839299199
3.65-3.820.2251100.14792872298299
3.82-4.020.18451460.142769291597
4.02-4.270.19521470.13292606275392
4.27-4.60.17661330.12362887302099
4.6-5.060.17371790.12712829300899
5.06-5.790.21051350.15082883301899
5.79-7.290.20041350.17342858299398
7.29-47.540.20751330.1662741287493

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