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- PDB-4bj1: Crystal structure of Saccharomyces cerevisiae RIF2 -

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Basic information

Entry
Database: PDB / ID: 4bj1
TitleCrystal structure of Saccharomyces cerevisiae RIF2
ComponentsPROTEIN RIF2
KeywordsDNA BINDING PROTEIN / GENOME STABILITY / TELOMERE ASSOCIATED PROTEINS / AAA+ FOLD
Function / homology
Function and homology information


shelterin complex / telomere capping / telomeric DNA binding / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1650 / Rossmann fold - #12060 / : / : / RIF2, ASCE domain / RIF2, AAA+ lid domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1650 / Rossmann fold - #12060 / : / : / RIF2, ASCE domain / RIF2, AAA+ lid domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 Å
AuthorsShi, T. / Bunker, R.D. / Gut, H. / Scrima, A. / Thoma, N.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Rif1 and Rif2 Shape Telomere Funcation and Architecture Through Multivalent RAP1 Interactions
Authors: Shi, T. / Bunker, R.D. / Mattarocci, S. / Ribeyre, C. / Faty, M. / Gut, H. / Scrima, A. / Rass, U. / Rubin, S.M. / Shore, D. / Thoma, N.H.
History
DepositionApr 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN RIF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8362
Polymers36,8001
Non-polymers351
Water362
1
A: PROTEIN RIF2
hetero molecules

A: PROTEIN RIF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6724
Polymers73,6012
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3380 Å2
ΔGint-39.5 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.360, 78.360, 236.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROTEIN RIF2 / RAP1-INTERACTING FACTOR 2


Mass: 36800.336 Da / Num. of mol.: 1 / Fragment: RESIDUES 65-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PGEX BASED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06208
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.43 Å3/Da / Density % sol: 0.64 % / Description: NONE
Crystal growDetails: 14-20% 1,4-BUTANEDIOL, 100 MM NA ACETATE PH 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 17, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→44.5 Å / Num. obs: 9796 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 105.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.8
Reflection shellResolution: 2.94→2.95 Å / Redundancy: 8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.94→38.65 Å / Cor.coef. Fo:Fc: 0.9396 / Cor.coef. Fo:Fc free: 0.9311 / SU R Cruickshank DPI: 0.696 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.881 / SU Rfree Blow DPI: 0.314 / SU Rfree Cruickshank DPI: 0.31
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 452 4.61 %RANDOM
Rwork0.1971 ---
obs0.1986 9795 99.61 %-
Displacement parametersBiso mean: 95.39 Å2
Baniso -1Baniso -2Baniso -3
1--6.782 Å20 Å20 Å2
2---6.782 Å20 Å2
3---13.564 Å2
Refine analyzeLuzzati coordinate error obs: 0.497 Å
Refinement stepCycle: LAST / Resolution: 2.94→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 1 2 2088
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012124HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.162872HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d734SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes298HARMONIC5
X-RAY DIFFRACTIONt_it2124HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion20.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion292SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2466SEMIHARMONIC4
LS refinement shellResolution: 2.94→3.29 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2878 115 4.27 %
Rwork0.2186 2579 -
all0.2216 2694 -
obs--99.61 %
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)
12.6528-2.3188-2.10922.57190.34937.3817-0.06230.3147-0.4855-0.2255-0.12510.0221-0.4326-0.5930.18740.0504-0.0204-0.0962-0.06480.0401-0.163729.723721.519719.2521
22.2323-4.7475-2.761312.09665.12716.8865-0.3793-0.37440.0117-0.26580.68880.2206-0.41640.3591-0.3094-0.16030.06080.1505-0.01110.1173-0.115424.777425.41940.8156
32.8888-1.4138-3.44889.04072.43455.3811-0.4597-0.6268-0.4130.90640.11960.78790.76370.14470.340.02650.20640.26870.09650.1426-0.10621.284720.087847.9521
43.9107-0.3907-2.23932.42010.43294.0338-0.03830.1863-0.7111-0.401-0.17660.34270.6716-0.09570.21490.0377-0.052-0.0557-0.22760.0665-0.141334.87510.426215.4224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|68 - 103 }
2X-RAY DIFFRACTION2{ A|104 - 205 }
3X-RAY DIFFRACTION3{ A|206 - 269 }
4X-RAY DIFFRACTION4{ A|270 - 373 }

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