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- PDB-2e11: The Crystal Structure of XC1258 from Xanthomonas campestris: A CN... -

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Basic information

Entry
Database: PDB / ID: 200000000000
TitleThe Crystal Structure of XC1258 from Xanthomonas campestris: A CN-hydrolase Superfamily Protein with an Arsenic Adduct in the Active Site
ComponentsHydrolase
KeywordsHYDROLASE / CN hydrolase / Xanthomonas campestris / dimethylarsenic inhibitor complex / cacodylate
Function / homology
Function and homology information


2-oxoglutaramate amidase activity / omega-amidase activity / :
Similarity search - Function
Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Hydrolase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.73 Å
AuthorsChin, K.-H. / Tsai, Y.-D. / Chan, N.-L. / Huang, K.-F. / Wang, A.H.-J. / Chou, S.-H.
CitationJournal: Proteins / Year: 2007
Title: The crystal structure of XC1258 from Xanthomonas campestris: A putative procaryotic Nit protein with an arsenic adduct in the active site
Authors: Chin, K.-H. / Tsai, Y.-D. / Chan, N.-L. / Huang, K.-F. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionOct 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrolase
B: Hydrolase
C: Hydrolase
D: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7918
Polymers120,2434
Non-polymers5484
Water13,331740
1
A: Hydrolase
C: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3964
Polymers60,1222
Non-polymers2742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-11 kcal/mol
Surface area19280 Å2
MethodPISA, PQS
2
B: Hydrolase
D: Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3964
Polymers60,1222
Non-polymers2742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-10 kcal/mol
Surface area19140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.280, 154.305, 51.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Hydrolase /


Mass: 30060.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: pv. campestris / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8P8M3, Hydrolases
#2: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 8

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97905, 0.96108
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979051
20.961081
ReflectionResolution: 1.73→104.83 Å / Num. obs: 112277 / % possible obs: 98.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.04 / Net I/σ(I): 9
Reflection shellResolution: 1.73→104.83 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9.1 / Num. unique all: 11276 / Rsym value: 0.14 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
DENZOdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.73→104.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.966 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 2 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21746 5865 5 %RANDOM
Rwork0.14 ---
all0.18789 ---
obs0.18636 110854 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.73→104.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8452 0 16 740 9208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218678
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.93111788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95922.696460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.407151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9661596
X-RAY DIFFRACTIONr_chiral_restr0.0980.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026856
X-RAY DIFFRACTIONr_nbd_refined0.2050.24259
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25915
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2579
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.216
X-RAY DIFFRACTIONr_mcbond_it0.8041.55367
X-RAY DIFFRACTIONr_mcangle_it1.33628404
X-RAY DIFFRACTIONr_scbond_it2.28733773
X-RAY DIFFRACTIONr_scangle_it3.4644.53384
LS refinement shellResolution: 1.726→1.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 397 -
Rwork0.21 7610 -
obs-11276 91.09 %

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