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- PDB-2gsc: Crystal Structure of the Conserved Hypothetical Cytosolic Protein... -

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Basic information

Entry
Database: PDB / ID: 2gsc
TitleCrystal Structure of the Conserved Hypothetical Cytosolic Protein Xcc0516 from Xanthomonas campestris
ComponentsPutative uncharacterized protein XCC0516
KeywordsUNKNOWN FUNCTION / four-helix bundle / homopentamer / pentameric toroid
Function / homology23S rRNA-intervening sequence protein / 23S rRNA-intervening sequence superfamily / 23S rRNA-intervening sequence protein / 23S rRNA-intervening sequence / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsLin, L.Y. / Ching, C.L. / Chin, K.H. / Chou, S.H. / Chan, N.L.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of the conserved hypothetical cytosolic protein Xcc0516 from Xanthomonas campestris reveals a novel quaternary structure assembled by five four-helix bundles.
Authors: Lin, L.Y. / Ching, C.L. / Chin, K.H. / Chou, S.H. / Chan, N.L.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein XCC0516
B: Putative uncharacterized protein XCC0516
C: Putative uncharacterized protein XCC0516
D: Putative uncharacterized protein XCC0516
E: Putative uncharacterized protein XCC0516


Theoretical massNumber of molelcules
Total (without water)73,1025
Polymers73,1025
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-8 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.794, 104.257, 66.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-129-

HOH

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Components

#1: Protein
Putative uncharacterized protein XCC0516 / conserved hypothetical protein / Conserved Hypothetical Cytosolic Protein Xcc0516


Mass: 14620.450 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PD29
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200mM KCl, 5mM MgCl2, 50mM Na cacodylate pH 6.0, 16%(w/v) 1,6-hexanediol, 100mM CsCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9537, 0.97991, 0.97972
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2005
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.979911
30.979721
ReflectionResolution: 2.45→30 Å / Num. all: 23060 / Num. obs: 22715 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.7
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.146 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.45→28.17 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.859 / SU B: 9.218 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.711 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1157 5.2 %RANDOM
Rwork0.22 ---
all0.223 23060 --
obs0.22 22463 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.148 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2--1.35 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 0 85 4633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214609
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9666214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36621.811243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57415822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6781577
X-RAY DIFFRACTIONr_chiral_restr0.0830.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023522
X-RAY DIFFRACTIONr_nbd_refined0.2110.22211
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.236
X-RAY DIFFRACTIONr_mcbond_it0.6251.52922
X-RAY DIFFRACTIONr_mcangle_it1.05124525
X-RAY DIFFRACTIONr_scbond_it1.60831897
X-RAY DIFFRACTIONr_scangle_it2.6794.51689
LS refinement shellResolution: 2.451→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 73 -
Rwork0.2 1419 -
obs-1492 100 %

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