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- PDB-1z1a: S. cerevisiae Sir1 ORC-interaction domain -

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Basic information

Entry
Database: PDB / ID: 1z1a
TitleS. cerevisiae Sir1 ORC-interaction domain
ComponentsRegulatory protein SIR1
KeywordsTRANSCRIPTION / novel fold
Function / homologySir1, ORC-binding domain / ORC1-binding domain / Sir1, ORC-binding domain / chromatin silencing complex / silent mating-type cassette heterochromatin formation / chromosome, centromeric region / heterochromatin formation / Regulatory protein SIR1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHou, Z. / Bernstein, D.A. / Fox, C.A. / Keck, J.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing.
Authors: Hou, Z. / Bernstein, D.A. / Fox, C.A. / Keck, J.L.
History
DepositionMar 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein SIR1
B: Regulatory protein SIR1


Theoretical massNumber of molelcules
Total (without water)33,6922
Polymers33,6922
Non-polymers00
Water77543
1
A: Regulatory protein SIR1


Theoretical massNumber of molelcules
Total (without water)16,8461
Polymers16,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein SIR1


Theoretical massNumber of molelcules
Total (without water)16,8461
Polymers16,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.928, 60.928, 159.257
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 Regulatory protein SIR1 / Silent information regulator 1


Mass: 16846.100 Da / Num. of mol.: 2 / Fragment: ORC-1 interacting domain of Sir1p / Mutation: C593A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR1 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P21691
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium acetate, PEG 400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9793, 0.9795, 0.9688
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2004
RadiationMonochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.96881
ReflectionResolution: 2.5→25 Å / Num. all: 11994 / Num. obs: 11994 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.665 / SU ML: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.494 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27424 1206 9.8 %RANDOM
Rwork0.23787 ---
all0.2414 11270 --
obs0.24148 11078 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.547 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0.7 Å20 Å2
2---1.39 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 43 1987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221990
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.9882685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825232
X-RAY DIFFRACTIONr_chiral_restr0.0710.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021454
X-RAY DIFFRACTIONr_nbd_refined0.2230.2757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.210
X-RAY DIFFRACTIONr_mcbond_it1.4371.51189
X-RAY DIFFRACTIONr_mcangle_it2.70321938
X-RAY DIFFRACTIONr_scbond_it2.5693801
X-RAY DIFFRACTIONr_scangle_it4.3474.5747
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 65
Rwork0.341 742
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)
12.89522.4155-0.07113.5566-0.4055-0.06870.0255-0.00250.1373-0.14740.13580.24820.03210.0978-0.16120.1654-0.09270.01040.08620.00190.120720.2308-1.544679.8657
22.0703-2.41151.31482.5970.11980.7754-0.0517-0.157-0.0237-0.04030.13930.08090.0688-0.0392-0.08770.20440.1047-0.10510.0865-0.02250.083912.711617.155247.7019
3-0.3441-0.34380.13610.6796-0.64641.24670.2814-0.0324-0.0286-0.0039-0.20010.15470.0268-0.1441-0.08130.1562-0.0259-0.00860.1326-0.02680.152720.34748.348366.8955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA484 - 61115 - 142
2X-RAY DIFFRACTION2BB486 - 61117 - 142
3X-RAY DIFFRACTION3BD1 - 43

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