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- PDB-2o0q: X-ray Crystal Structure of Protein CC0527 from Caulobacter cresce... -

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Basic information

Entry
Database: PDB / ID: 2o0q
TitleX-ray Crystal Structure of Protein CC0527 from Caulobacter crescentus. Northeast Structural Genomics Consortium Target CcR55
ComponentsHypothetical protein CC0527
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Hypothetical protein CC0527
Function / homologyProtein of unknown function DUF952 / Protein of unknown function DUF952 / Protein of unknown function (DUF952) / ADP-ribosylation fold / Alpha-Beta Barrel / Alpha Beta / DUF952 domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeetharaman, J. / Su, M. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Su, M. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the Hypothetical Protein from Caulobacter Crescentus.
Authors: Seetharaman, J. / Su, M. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 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: Hypothetical protein CC0527


Theoretical massNumber of molelcules
Total (without water)12,5711
Polymers12,5711
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.143, 104.326, 46.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Hypothetical protein CC0527


Mass: 12571.089 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AAR9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 4.07 Å3/Da / Density % sol: 69.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Sodium acetate, 0.1M Sodium Citrate, PGE 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2006 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 31132 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.054 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 9.4 / Num. unique all: 3267 / Rsym value: 0.334 / % possible all: 88.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O0P

2o0p


Resolution: 1.8→32.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 83262.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1548 5 %RANDOM
Rwork0.222 ---
obs0.222 31132 84.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6208 Å2 / ksol: 0.390814 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.94 Å20 Å20 Å2
2---3.18 Å20 Å2
3----3.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→32.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 0 152 1028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 184 5.5 %
Rwork0.231 3151 -
obs--54.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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