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- PDB-2f8h: Structure of acetylcitrulline deacetylase from Xanthomonas campes... -

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Basic information

Entry
Database: PDB / ID: 2f8h
TitleStructure of acetylcitrulline deacetylase from Xanthomonas campestris in metal-free form
Componentsaectylcitrulline deacetylase
KeywordsHYDROLASE / alpha/beta
Function / homology
Function and homology information


deacetylase activity / arginine biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / metal ion binding
Similarity search - Function
N-acetyl-L-citrulline deacetylase ArgE'-like / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...N-acetyl-L-citrulline deacetylase ArgE'-like / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-citrulline deacetylase / N-acetyl-L-citrulline deacetylase
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsShi, D. / Yu, X. / Roth, L. / Allewell, N.M. / Tuchman, M.
CitationJournal: Biophys.Chem. / Year: 2007
Title: Structure of a novel N-acetyl-L-citrulline deacetylase from Xanthomonas campestris
Authors: Shi, D. / Yu, X. / Roth, L. / Tuchman, M. / Allewell, N.M.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aectylcitrulline deacetylase


Theoretical massNumber of molelcules
Total (without water)39,1661
Polymers39,1661
Non-polymers00
Water6,323351
1
A: aectylcitrulline deacetylase

A: aectylcitrulline deacetylase


Theoretical massNumber of molelcules
Total (without water)78,3322
Polymers78,3322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)94.133, 95.226, 43.613
Angle α, β, γ (deg.)90.00, 93.76, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z+1.

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Components

#1: Protein aectylcitrulline deacetylase / E.C.3.5.1.16 / acetylornithine deacetylase


Mass: 39165.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Strain: ATCC 33913 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4UVI8, UniProt: A0A0H2X6W0*PLUS, acetylornithine deacetylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 12-15% (w/v) PEG 3350, 200 mM magnesium formate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→35.72 Å / Num. all: 37941 / Num. obs: 37941 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3716 / % possible all: 96

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F7V

2f7v


Resolution: 1.75→35.72 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1545547.5 / 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
Rfree0.258 1889 5 %RANDOM
Rwork0.226 ---
all0.229 37941 --
obs0.229 37898 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.1542 Å2 / ksol: 0.370745 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å20 Å25.07 Å2
2---0.59 Å20 Å2
3---3.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.75→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 0 351 3048
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
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_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 317 5.1 %
Rwork0.307 5890 -
obs--96.7 %
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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