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- PDB-3kzk: Crystal structure of acetylornithine transcarbamylase complexed w... -

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Basic information

Entry
Database: PDB / ID: 3kzk
TitleCrystal structure of acetylornithine transcarbamylase complexed with acetylcitrulline
ComponentsN-acetylornithine carbamoyltransferase
KeywordsTRANSFERASE / transcarbamylase / Amino-acid biosynthesis / Arginine biosynthesis / Cytoplasm
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
(S)-2-ACETAMIDO-5-UREIDOPENTANOIC ACID / N-acetylornithine carbamoyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShi, D. / Yu, X. / Allewell, N.M. / Tuchman, M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of N-acetylornithine transcarbamylase from Xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several eubacteria.
Authors: Shi, D. / Morizono, H. / Yu, X. / Roth, L. / Caldovic, L. / Allewell, N.M. / Malamy, M.H. / Tuchman, M.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMar 31, 2010ID: 1YH1
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: N-acetylornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5434
Polymers40,1341
Non-polymers4093
Water2,612145
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)121,62912
Polymers120,4013
Non-polymers1,2289
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 area10420 Å2
ΔGint-162 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.446, 129.446, 129.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 40133.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / 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-OLN / (S)-2-ACETAMIDO-5-UREIDOPENTANOIC ACID / N-ACETYL-L-CITRULLINE


Mass: 217.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15N3O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 45.38 %
Crystal growTemperature: 291 K / pH: 7.5
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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 28507 / Num. obs: 28390 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.2 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AKM

1akm


Resolution: 1.9→40.94 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.33 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.247 2818 9.9 %
Rwork0.219 --
obs0.219 28390 99.5 %
all-28507 -
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.44 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 35.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 25 145 2802
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.318 475 10.2 %
Rwork0.263 4172 -
obs--99.4 %
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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