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- PDB-2o6w: Crystal Structure of a Pentapeptide Repeat Protein (Rfr23) from t... -

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Basic information

Entry
Database: PDB / ID: 2o6w
TitleCrystal Structure of a Pentapeptide Repeat Protein (Rfr23) from the cyanobacterium Cyanothece 51142
ComponentsRepeat Five Residue (Rfr) protein or pentapeptide repeat protein
KeywordsUNKNOWN FUNCTION / Rfr protein / pentapeptide repeat protein / beta helix
Function / homology: / Pentapeptide repeats (8 copies) / Pentapeptide repeat / ARSENIC / Repeat Five Residue (Rfr) protein or pentapeptide repeat protein
Function and homology information
Biological speciesCyanothece (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKennedy, M.A. / Buchko, G.W. / Ni, S. / Robinson, H. / Pakrasi, H.B.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Insights into the structural variation between pentapeptide repeat proteins-Crystal structure of Rfr23 from Cyanothece 51142.
Authors: Buchko, G.W. / Robinson, H. / Pakrasi, H.B. / Kennedy, M.A.
History
DepositionDec 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repeat Five Residue (Rfr) protein or pentapeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6062
Polymers16,5311
Non-polymers751
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.391, 106.391, 52.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-1-

ARS

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Components

#1: Protein Repeat Five Residue (Rfr) protein or pentapeptide repeat protein


Mass: 16531.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece (bacteria) / Genus: Cyanothece / Strain: 51142 / Gene: Rfr23 / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: D0VWX3*PLUS
#2: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.192 magnesium acetate, 0.096M sodium cacodylate, 10%(w/v) PEG 8000, 10%(w/v) glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2005
Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 16261 / % possible obs: 89.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Rsym value: 0.12 / Net I/σ(I): 42.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 4.53 / Num. unique all: 1159 / Rsym value: 0.335 / % possible all: 61.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1513 -random
Rwork0.2507 ---
obs-16261 85.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.641 Å2--
2--15.641 Å2-
3----31.282 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 1 62 1192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006295
X-RAY DIFFRACTIONx_angle_deg1.07784
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.2637 1513 -
Rwork0.2507 --
obs-28646 85.4 %

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