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- PDB-8qeu: Crystal structure of ornithine transcarbamylase from Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 8qeu
TitleCrystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with ornithine
ComponentsOrnithine transcarbamylase, chloroplastic
KeywordsTRANSFERASE / transcarbamylase / carbamoyl transferase / urea cycle / arginine biosynthesis
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / L-arginine biosynthetic process / chloroplast stroma / amino acid binding / chloroplast
Similarity search - Function
Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / 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
L-ornithine / DI(HYDROXYETHYL)ETHER / Ornithine transcarbamylase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNielipinski, M. / Pietrzyk-Brzezinska, A. / Sekula, B.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2021/43/D/NZ1/00486 Poland
CitationJournal: Front Plant Sci / Year: 2023
Title: Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae .
Authors: Nielipinski, M. / Pietrzyk-Brzezinska, A.J. / Wlodawer, A. / Sekula, B.
History
DepositionSep 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine transcarbamylase, chloroplastic
B: Ornithine transcarbamylase, chloroplastic
C: Ornithine transcarbamylase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,51332
Polymers107,2533
Non-polymers2,26029
Water23,0231278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.307, 155.380, 189.541
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-406-

SO4

21B-750-

HOH

31B-891-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 35750.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: OTC, At1g75330, F1B16.13
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O50039, ornithine carbamoyltransferase

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Non-polymers , 6 types, 1307 molecules

#2: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350 16%, Lithium sulfate 0.3M, HEPES 0.1M pH 6.0, 20mM ornithine, cryoprotection was obtained by 25% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 208445 / % possible obs: 99.6 % / Redundancy: 7.33 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.88
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 33258 / CC1/2: 0.731 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.02 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.299 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15603 1043 0.5 %RANDOM
Rwork0.11927 ---
obs0.11945 207402 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å20 Å2
2---0.21 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.5→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7189 0 66 1278 8533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127562
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167278
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.65310221
X-RAY DIFFRACTIONr_angle_other_deg0.6221.5816793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.556541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2101339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5481.8943724
X-RAY DIFFRACTIONr_mcbond_other1.5481.8943724
X-RAY DIFFRACTIONr_mcangle_it2.1743.4284661
X-RAY DIFFRACTIONr_mcangle_other2.1743.4284662
X-RAY DIFFRACTIONr_scbond_it1.9412.2073838
X-RAY DIFFRACTIONr_scbond_other1.9422.2083839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5163.8965535
X-RAY DIFFRACTIONr_long_range_B_refined4.38822.858775
X-RAY DIFFRACTIONr_long_range_B_other3.62719.528316
X-RAY DIFFRACTIONr_rigid_bond_restr4.273314840
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 77 -
Rwork0.301 15255 -
obs--99.62 %

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