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- PDB-2f3l: Crystal Structure of a Lumenal Rfr-domain protein (Contig83.1_1_2... -

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Basic information

Entry
Database: PDB / ID: 2f3l
TitleCrystal Structure of a Lumenal Rfr-domain protein (Contig83.1_1_243_746) from Cyanothece sp. 51142 at 2.1 Angstrom resolution.
ComponentsRFR-Domain
KeywordsUNKNOWN FUNCTION / Beta Helix
Function / homologyThylakoid lumenal 15kDa protein 1-like / Pentapeptide repeats (8 copies) / plasma membrane-derived thylakoid lumen / E3 ubiquitin-protein ligase SopA / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / Pentapeptide repeat protein Rfr32
Function and homology information
Biological speciesCyanothece sp. ATCC 51142 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsKennedy, M.A. / Ni, S. / Buchko, G.W. / Robinson, H.
CitationJournal: Protein Sci. / Year: 2006
Title: Characterization of two potentially universal turn motifs that shape the repeated five-residues fold-Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142.
Authors: Buchko, G.W. / Ni, S. / Robinson, H. / Welsh, E.A. / Pakrasi, H.B. / Kennedy, M.A.
History
DepositionNov 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS FILE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RFR-Domain


Theoretical massNumber of molelcules
Total (without water)20,1191
Polymers20,1191
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.754, 61.754, 83.708
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RFR-Domain


Mass: 20119.174 Da / Num. of mol.: 1
Fragment: full-length Rfr-domain protein minus N-terminal 29 residues predicted to be a signal peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. ATCC 51142 (bacteria) / Strain: BH68 / Gene: Rfr-domain protein / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS / References: UniProt: B1WVN5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 15% PEG 1500, 50 mM sodium chloride, 10 mM Tris, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.979
SYNCHROTRONNSLS X29A21.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDOct 18, 2005Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
ADSC QUANTUM 42CCDOct 17, 2005Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.11
ReflectionResolution: 2.11→50 Å / Num. all: 11820 / Num. obs: 9861 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 25.2
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 3.56 / Num. unique all: 613 / Rsym value: 0.218 / % possible all: 57.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.11→50 Å / Cross valid method: random / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 485 -random
Rwork0.2168 ---
all0.2168 9835 --
obs0.2168 9549 85.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.311 Å2-2.328 Å20 Å2
2---8.311 Å20 Å2
3---16.621 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 0 25 1013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006188
X-RAY DIFFRACTIONc_angle_deg1.00337

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