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- PDB-3m5c: Crystal structure of N-acetyl-L-ornithine transcarbamylase K302E ... -

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Basic information

Entry
Database: PDB / ID: 3m5c
TitleCrystal structure of N-acetyl-L-ornithine transcarbamylase K302E mutant complexed with PALAO
ComponentsN-acetylornithine carbamoyltransferase
KeywordsTRANSFERASE / transcarbamylase
Function / homology
Function and homology information


N-acetylornithine carbamoyltransferase / N-acetylornithine carbamoyltransferase activity / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / amino acid binding / cytoplasm
Similarity search - Function
N-acetylornithine carbamoyltransferase ArgF'-like / Aspartate/ornithine 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N~2~-acetyl-N~5~-(phosphonoacetyl)-L-ornithine / N-acetylornithine carbamoyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLi, Y. / Yu, X. / Allewell, N.M. / Tuchman, M. / Shi, D.
CitationJournal: Biochemistry / Year: 2010
Title: Reversible post-translational carboxylation modulates the enzymatic activity of N-acetyl-L-ornithine transcarbamylase.
Authors: Li, Y. / Yu, X. / Ho, J. / Fushman, D. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations / Category: 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 1.4Sep 6, 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

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Assembly

Deposited unit
A: N-acetylornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4833
Polymers40,0911
Non-polymers3922
Water3,477193
1
A: N-acetylornithine carbamoyltransferase
hetero molecules

A: N-acetylornithine carbamoyltransferase
hetero molecules

A: N-acetylornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4489
Polymers120,2723
Non-polymers1,1776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area9680 Å2
ΔGint-93 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.288, 129.288, 129.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-350-

SO4

21A-350-

SO4

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Components

#1: Protein N-acetylornithine carbamoyltransferase / / AOTCase


Mass: 40090.504 Da / Num. of mol.: 1 / Mutation: K302E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: argF, argF', XCC2249 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8P8J2, N-acetylornithine carbamoyltransferase
#2: Chemical ChemComp-PA9 / N~2~-acetyl-N~5~-(phosphonoacetyl)-L-ornithine


Mass: 296.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N2O7P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Lithium sulfate, Bis-tris, PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 4, 2009
RadiationMonochromator: FOCUS MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 30622 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.052 / Χ2: 0.989 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.885.40.55314561.05395.1
1.88-1.926.40.48115041.05798.1
1.92-1.957.60.40414941.09499.9
1.95-1.999.40.34815371.152100
1.99-2.0412.50.30715201.184100
2.04-2.0813.90.26515230.956100
2.08-2.14140.22115220.925100
2.14-2.1914.10.18415240.919100
2.19-2.2614.10.15315340.908100
2.26-2.3314.20.1315550.912100
2.33-2.4114.30.11415000.925100
2.41-2.5114.40.09815160.906100
2.51-2.6214.40.08515430.935100
2.62-2.7614.40.07515190.984100
2.76-2.9414.40.06615600.955100
2.94-3.1614.40.05515390.986100
3.16-3.4814.40.04615461.052100
3.48-3.9814.20.03915410.95199.9
3.98-5.0214.20.03315671.097100
5.02-4013.40.02516221.05499.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M4J

3m4j


Resolution: 1.85→37.32 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.33 / Data cutoff high absF: 3740944 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1520 5 %RANDOM
Rwork0.2 ---
obs-30612 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.638 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 63.08 Å2 / Biso mean: 32.528 Å2 / Biso min: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.85→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 24 193 2833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.322.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 256 5.2 %
Rwork0.267 4703 -
all-4959 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top

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