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- PDB-2o0p: X-ray Crystal Structure of Protein CC0527 (V27M / L66M double mut... -

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Basic information

Entry
Database: PDB / ID: 2o0p
TitleX-ray Crystal Structure of Protein CC0527 (V27M / L66M double mutant) from Caulobacter crescentus. Northeast Structural Genomics Consortium Target CcR55.
ComponentsHypothetical protein CC0527Hypothesis
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 / SAD / Resolution: 1.9 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 27, 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)13,7201
Polymers13,7201
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.864, 103.773, 46.097
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 / Hypothesis


Mass: 13719.872 Da / Num. of mol.: 1 / Mutation: Yes
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 / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.7 Å3/Da / Density % sol: 66.73 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X3A10.978
SYNCHROTRONNSLS X4A20.978
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDNov 15, 2006
ADSC QUANTUM 42CCDNov 14, 2006Mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1SI 111 CHANNEL
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31207 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 9.04 / Num. unique all: 3118 / Rsym value: 0.369 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→32.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 128995.46 / 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
Rfree0.245 1320 4.8 %RANDOM
Rwork0.234 ---
obs0.234 27297 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2603 Å2 / ksol: 0.389844 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.43 Å20 Å20 Å2
2---2.44 Å20 Å2
3----1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 0 103 984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 175 4.5 %
Rwork0.248 3682 -
obs--74.6 %
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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