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- PDB-3l05: Crystal structure of N-acetyl-L-ornithine transcarbamylase E92S m... -

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Basic information

Entry
Database: PDB / ID: 3l05
TitleCrystal structure of N-acetyl-L-ornithine transcarbamylase E92S mutant complexed with carbamyl phosphate and N-succinyl-L-norvaline
ComponentsN-acetylornithine carbamoyltransferase
KeywordsTRANSFERASE / Transcarbamylase / Amino-acid biosynthesis / Arginine biosynthesis
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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / N-(3-CARBOXYPROPANOYL)-L-NORVALINE / N-acetylornithine carbamoyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShi, D. / Yu, X. / Allewell, N.M. / Tuchman, M.
CitationJournal: Protein Sci. / Year: 2007
Title: A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase.
Authors: Shi, D. / Yu, X. / Cabrera-Luque, J. / Chen, T.Y. / Roth, L. / Morizono, H. / Allewell, N.M. / Tuchman, M.
History
DepositionDec 9, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMar 31, 2010ID: 2G6A
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 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
Revision 1.5Nov 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5464
Polymers40,0921
Non-polymers4543
Water1,08160
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)121,63712
Polymers120,2753
Non-polymers1,3639
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 area10630 Å2
ΔGint-120 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.974, 128.974, 128.974
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: 40091.531 Da / Num. of mol.: 1 / Mutation: E92S
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-SN0 / N-(3-CARBOXYPROPANOYL)-L-NORVALINE


Mass: 217.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO5
#3: Chemical ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Carbamoyl phosphate


Mass: 141.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
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 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 8953 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 110.9 Å2 / Rmerge(I) obs: 0.153 / Χ2: 1.028 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 3.3 / Num. unique all: 875 / Χ2: 1.063 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KZO

3kzo


Resolution: 2.8→30.4 Å / Rfactor Rfree error: 0.012 / Occupancy max: 1 / Occupancy min: 0.33 / Data cutoff high absF: 2163796 / 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
Rfree0.265 492 5.5 %RANDOM
Rwork0.184 ---
obs-8930 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.582 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 70.96 Å2 / Biso mean: 38.489 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 28 60 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 70 4.8 %
Rwork0.266 1385 -
all-1455 -
obs--100 %
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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