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- PDB-4hce: Crystal structure of the telomeric Saccharomyces cerevisiae Cdc13... -

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Basic information

Entry
Database: PDB / ID: 4hce
TitleCrystal structure of the telomeric Saccharomyces cerevisiae Cdc13 OB2 domain
ComponentsCell division control protein 13
KeywordsCELL CYCLE / OB fold / oligonucleotide/oligosaccharide binding fold
Function / homology
Function and homology information


negative regulation of DNA duplex unwinding / CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping ...negative regulation of DNA duplex unwinding / CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region / cell division / identical protein binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #860 / 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 / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #860 / 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 / Protection of telomeres protein 1 / 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
Cell division control protein 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsMason, M. / Wannat, J.J. / Harper, S. / Schultz, D.C. / Speicher, D.W. / Johnson, F.B. / Skordalakes, E.
CitationJournal: Structure / Year: 2013
Title: Cdc13 OB2 Dimerization Required for Productive Stn1 Binding and Efficient Telomere Maintenance.
Authors: Mason, M. / Wanat, J.J. / Harper, S. / Schultz, D.C. / Speicher, D.W. / Johnson, F.B. / Skordalakes, E.
History
DepositionSep 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 13
B: Cell division control protein 13


Theoretical massNumber of molelcules
Total (without water)33,6712
Polymers33,6712
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-22 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.884, 78.770, 100.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division control protein 13


Mass: 16835.322 Da / Num. of mol.: 2 / Fragment: Cdc13 OB2, UNP residues 344-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CDC13, YDL220C / Production host: Escherichia coli (E. coli) / References: UniProt: P32797
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M NaCl, 0.1 M BIS-Tris pH 6.5, and 1.5 M AmSO4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1, 1.0005
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 6, 2011
ADSC QUANTUM 3152CCDApr 8, 2011
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.00051
ReflectionResolution: 2.3→40 Å / Num. all: 14202 / Num. obs: 14100 / % possible obs: 99.28 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.3→2.42 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.707 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.292 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24671 757 5.1 %RANDOM
Rwork0.20204 ---
obs0.20438 14100 99.28 %-
all-14202 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.689 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2---1.19 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 0 105 2140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022072
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9932816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.875257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.01225.47684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90515381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4151510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211510
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 43 -
Rwork0.244 881 -
obs--92.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35860.17660.07152.5456-1.42962.09920.0642-0.0018-0.0263-0.0353-0.09-0.08310.11110.05170.02570.0780.00930.02840.04950.02650.1308-16.036-5.20713.045
20.47530.0073-0.41611.05270.27961.5410.00750.01150.00250.14130.0042-0.02850.1092-0.0041-0.01180.0941-0.0229-0.01320.09490.01170.1111-21.13414.94912.691
30.063-0.29850.02531.78780.0150.062-0.00540.01340.03010.1659-0.07770.01680.03060.00570.08310.0888-0.03310.01040.19670.02720.1177-19.6097.76214.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A346 - 474
2X-RAY DIFFRACTION2B346 - 474
3X-RAY DIFFRACTION3A501 - 540
4X-RAY DIFFRACTION3B501 - 565

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