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- PDB-2e12: The crystal structure of XC5848 from Xanthomonas campestris adopt... -

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Basic information

Entry
Database: PDB / ID: 2000000000000
TitleThe crystal structure of XC5848 from Xanthomonas campestris adopting a novel variant of Sm-like motif
ComponentsHypothetical protein XCC3642
KeywordsTRANSLATION / novel Sm-like motif / Lsm motif / Xanthomonas campestris
Function / homologyProtein of unknown function (DUF3247) / Protein of unknown function DUF3247 / Protein of unknown function (DUF3247) / SH3 type barrels. / Roll / Mainly Beta / DUF3247 family protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsChin, K.-H. / Ruan, S.-K. / Wang, A.H.-J. / Chou, S.-H.
CitationJournal: Proteins / Year: 2007
Title: XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif
Authors: Chin, K.-H. / Ruan, S.-K. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionOct 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein XCC3642
B: Hypothetical protein XCC3642


Theoretical massNumber of molelcules
Total (without water)23,1422
Polymers23,1422
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.942, 51.699, 82.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein XCC3642 / Sm-like motif


Mass: 11571.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: pv. campestris / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P4R5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96437, 0.97983
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.964371
20.979831
ReflectionResolution: 1.7→30 Å / Num. obs: 6937 / % possible obs: 99.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.24 / Rsym value: 0.06 / Net I/σ(I): 8
Reflection shellHighest resolution: 1.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 7.9 / Num. unique all: 6937 / Rsym value: 0.24 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 --random
Rwork0.22 ---
all0.27 ---
obs0.24 6937 99.1 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 0 122 1634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006869
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_deg1.31537
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.75 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.22 --
Rwork0.24 --
obs-6937 97 %

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