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- PDB-3rmh: Crystal Structure of yeast telomere protein Cdc13 OB4 -

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Basic information

Entry
Database: PDB / ID: 3rmh
TitleCrystal Structure of yeast telomere protein Cdc13 OB4
ComponentsYeast Cdc13 OB4
KeywordsPROTEIN BINDING / OB fold / dimer / dimeric complex
Function / homology
Function and homology information


chromosome, telomeric region => GO:0000781 / telomere maintenance / DNA binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #810 / Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #810 / Cell division control protein 13, OB2 domain / Cell division control protein 13, OB2 domain / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Telo_bind domain-containing protein
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.902 Å
AuthorsSun, J. / Yang, Y. / Lei, M.
CitationJournal: Mol.Cell.Biol. / Year: 2012
Title: Analyses of Candida Cdc13 Orthologues Revealed a Novel OB Fold Dimer Arrangement, Dimerization-Assisted DNA Binding, and Substantial Structural Differences between Cdc13 and RPA70.
Authors: Yu, E.Y. / Sun, J. / Lei, M. / Lue, N.F.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Yeast Cdc13 OB4
B: Yeast Cdc13 OB4


Theoretical massNumber of molelcules
Total (without water)35,0882
Polymers35,0882
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-6 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.087, 39.046, 63.100
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Yeast Cdc13 OB4


Mass: 17544.146 Da / Num. of mol.: 2 / Mutation: M661L, A690V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0G05588g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FT40
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 277 K / Method: sitting drop / pH: 7.4
Details: 28%PEG4000, 0.1M Tris-HCl, 0.01M NH4Cl, 0.05M CaCl2, pH 7.4, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 17, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 22461 / % possible obs: 98.31 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.902→29.859 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1155 5.14 %
Rwork0.2059 --
obs0.2076 22461 98.31 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.417 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4633 Å20 Å22.6731 Å2
2--8.3663 Å2-0 Å2
3---1.097 Å2
Refinement stepCycle: LAST / Resolution: 1.902→29.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 132 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072214
X-RAY DIFFRACTIONf_angle_d1.0753008
X-RAY DIFFRACTIONf_dihedral_angle_d12.921848
X-RAY DIFFRACTIONf_chiral_restr0.07357
X-RAY DIFFRACTIONf_plane_restr0.004382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.902-1.98820.25321160.21932420X-RAY DIFFRACTION90
1.9882-2.0930.24961590.20042667X-RAY DIFFRACTION99
2.093-2.2240.24511260.20392692X-RAY DIFFRACTION100
2.224-2.39570.24221410.19672683X-RAY DIFFRACTION100
2.3957-2.63670.25251590.21752692X-RAY DIFFRACTION100
2.6367-3.01790.24411290.21222729X-RAY DIFFRACTION100
3.0179-3.8010.25291720.2032687X-RAY DIFFRACTION100
3.801-29.86250.21471530.20362736X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -15.3223 Å / Origin y: -6.8937 Å / Origin z: 0.2205 Å
111213212223313233
T0.1109 Å2-0.0178 Å2-0.0041 Å2-0.1155 Å2-0.0256 Å2--0.1258 Å2
L1.5741 °20.0025 °2-0.7555 °2-0.4653 °20.1484 °2--5.0661 °2
S0.0784 Å °-0.0137 Å °0.0722 Å °-0.0306 Å °-0.1131 Å °0.0334 Å °-0.023 Å °-0.1263 Å °0.0263 Å °
Refinement TLS groupSelection details: ALL

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