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- PDB-5eyb: X-ray Structure of Reb1-Ter Complex -

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Basic information

Entry
Database: PDB / ID: 5eyb
TitleX-ray Structure of Reb1-Ter Complex
Components
  • (DNA (26-MER)) x 2
  • DNA-binding protein reb1
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / transcription termination / replication termination / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / cis-acting DNA replication termination / rDNA spacer replication fork barrier binding, bending / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / replication fork arrest involved in DNA replication termination / transcription termination site sequence-specific DNA binding / replication fork arrest / rDNA heterochromatin / termination of RNA polymerase I transcription ...: / cis-acting DNA replication termination / rDNA spacer replication fork barrier binding, bending / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / replication fork arrest involved in DNA replication termination / transcription termination site sequence-specific DNA binding / replication fork arrest / rDNA heterochromatin / termination of RNA polymerase I transcription / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein reb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsJaiswal, R. / Choudhury, M. / Zaman, S. / Singh, S. / Santosh, V. / Bastia, D. / Escalante, C.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM092854 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21CA179008 United States
ACS-IRG11997-IRG-73-001-34-IRG United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM098013-04 United States
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Functional architecture of the Reb1-Ter complex of Schizosaccharomyces pombe.
Authors: Jaiswal, R. / Choudhury, M. / Zaman, S. / Singh, S. / Santosh, V. / Bastia, D. / Escalante, C.R.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2015
Title: Crystallization and preliminary X-ray characterization of the eukaryotic replication termination Reb1-Ter DNA complex
Authors: Jaiswal, R. / Singh, S.K. / Bastia, D. / Escalante, C.R.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein reb1
C: DNA (26-MER)
D: DNA (26-MER)
B: DNA-binding protein reb1
E: DNA (26-MER)
F: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)118,0456
Polymers118,0456
Non-polymers00
Water2,324129
1
A: DNA-binding protein reb1
C: DNA (26-MER)
D: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)59,0223
Polymers59,0223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-54 kcal/mol
Surface area24540 Å2
MethodPISA
2
B: DNA-binding protein reb1
E: DNA (26-MER)
F: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)59,0223
Polymers59,0223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-50 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.959, 162.911, 71.086
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-binding protein reb1


Mass: 43051.082 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 146-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: reb1, SPBC1198.11c, SPBC660.01c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9P6H9
#2: DNA chain DNA (26-MER)


Mass: 8090.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 7881.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 298 K / Method: microbatch
Details: AMMONIUM SULFATE, PEG 5000 MME, MES, MICROBATCH, TEMPERATURE 293K
PH range: 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9762, 0.979
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.9791
ReflectionResolution: 2.7→50 Å / Num. obs: 42323 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 71.37 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.645 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→32.49 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 2072 4.92 %
Rwork0.21 --
obs0.212 42149 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 2120 0 129 7618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037882
X-RAY DIFFRACTIONf_angle_d0.57211128
X-RAY DIFFRACTIONf_dihedral_angle_d20.3012982
X-RAY DIFFRACTIONf_chiral_restr0.0241220
X-RAY DIFFRACTIONf_plane_restr0.0021057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7023-2.76510.36781340.34332629X-RAY DIFFRACTION96
2.7651-2.83430.35991510.32232639X-RAY DIFFRACTION100
2.8343-2.91080.31221370.30252703X-RAY DIFFRACTION100
2.9108-2.99640.36271560.30332712X-RAY DIFFRACTION100
2.9964-3.09310.31161460.27152658X-RAY DIFFRACTION99
3.0931-3.20350.24121260.25342665X-RAY DIFFRACTION98
3.2035-3.33170.2871490.24192645X-RAY DIFFRACTION98
3.3317-3.48320.30611340.22432644X-RAY DIFFRACTION98
3.4832-3.66660.24511510.21272677X-RAY DIFFRACTION100
3.6666-3.89590.22521210.20652716X-RAY DIFFRACTION100
3.8959-4.19620.22531420.18772729X-RAY DIFFRACTION100
4.1962-4.61740.22631270.18252721X-RAY DIFFRACTION100
4.6174-5.2830.19331440.19182699X-RAY DIFFRACTION100
5.283-6.64670.22631310.19232723X-RAY DIFFRACTION100
6.6467-32.48850.211230.17532517X-RAY DIFFRACTION91
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)
16.94987.19780.22279.94782.24042.84350.0271-0.7483-0.19390.1967-0.19230.2027-0.3531-0.17940.15140.51990.1098-0.05420.54840.06910.4195-16.2921-20.722579.4941
25.3468-1.2458-4.26173.17653.2548.64920.19490.43050.27810.015-0.22240.3785-0.3902-0.99560.06520.63060.0917-0.09130.66360.02030.3934-7.08933.440162.7568
37.8829-6.18212.74625.5707-2.51251.923-0.0184-0.3775-0.8603-0.04160.18450.34660.1503-0.2514-0.17190.5636-0.08870.01360.5360.05540.630921.9597-24.621569.5903
43.44741.4285-0.45534.9062-3.19851.54830.0755-0.1268-0.38120.2028-0.3351-0.7413-0.0048-0.01460.23860.74120.07130.03590.4893-0.00720.38691.5262-7.075370.0043
53.00092.7315-0.24726.83610.90881.6440.1183-0.0174-0.4658-1.12480.0507-0.10640.30640.1102-0.17921.07650.03620.02620.50510.05021.1019-4.2953-34.294370.0614
66.32092.5858-3.01855.9196-2.57034.38740.19420.0561-0.2122-0.2106-0.5622-0.227-0.19910.15480.31990.68040.1087-0.0390.5467-0.06440.4114.3562-0.031668.0306
72.10931.1353-1.54494.0338-1.58862.78661.19121.17032.0184-1.2727-0.8488-0.9439-1.2876-0.1876-0.20021.42280.10490.07410.59630.16050.79050.996421.371564.8355
89.6764-1.9796-0.78981.3297-1.29043.48440.6785-0.5181.1853-1.42220.4741-1.7524-2.456-0.8346-1.09451.3380.22670.19560.62010.01231.0293-3.413525.461772.4213
97.0946-2.32484.66822.84311.44237.5883-0.31172.0284-1.681-0.66630.53170.12290.1482-0.1285-0.21290.6009-0.31430.14681.197-0.35550.851210.4481-12.414997.7812
100.7235-2.55431.78388.6153-5.76124.61410.49860.0263-0.3342-1.3365-0.02380.87391.00340.3538-0.56080.852-0.1269-0.08961.0774-0.34650.92416.5107-36.3877103.643
111.30790.81050.5523.7231-1.48822.4469-0.00210.0803-0.4002-0.0438-0.0386-0.4902-0.2004-0.13560.05160.61290.01090.10080.5434-0.15980.772331.9722-32.9031116.1383
127.22632.53141.46843.15751.65252.4026-0.30010.4506-0.1208-0.02310.21490.1407-0.456-0.1180.09610.562-0.03970.02730.5994-0.0150.33354.8164-6.6689103.3957
131.18520.11321.16612.0866-1.42951.6490.62890.1139-0.2907-0.0175-0.5426-1.18280.41950.0693-0.140.9825-0.06680.26630.6368-0.15631.441435.2564-46.231106.9441
145.2989-2.95414.40582.5303-1.98993.87391.22291.96891.07420.8283-1.5179-0.21011.6504-0.63830.25520.84050.0160.06520.7252-0.1730.956126.0985-18.0304104.9469
157.006-0.68130.60322.0956-1.90093.9729-0.28790.77070.79260.7706-0.2657-1.1416-0.30870.0590.54390.9516-0.1693-0.0470.5863-0.02230.948426.24820.1909107.1091
162.9346-1.5174-4.20292.93112.47036.04360.42560.2262-0.28473.5213-0.4563-0.9591-0.524-0.91540.11811.35960.02950.05890.61740.11590.973518.17455.5146110.4331
179.0579-8.0452-3.66299.83952.16427.3039-0.64092.2289-0.76710.11330.3324-0.770.3162-0.06810.27850.5992-0.16820.21220.8248-0.23981.189530.1022-6.0711103.123
181.2789-0.03641.10375.96495.51136.1319-0.2878-0.7761-1.4023-0.4164-0.5163-1.07940.4517-0.45950.73090.6783-0.09330.34590.6612-0.13811.021529.8784-22.0473110.9701
193.59141.70382.83147.52660.01442.47280.77170.0545-0.6874-0.3909-0.5053-1.05860.5451-0.1586-0.29661.1128-0.00420.30670.6313-0.23621.203834.2744-49.1865107.4004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 154 THROUGH 242 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 243 THROUGH 340 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 341 THROUGH 500 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 1 THROUGH 26 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID 1 THROUGH 11 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID 12 THROUGH 22 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 23 THROUGH 24 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 25 THROUGH 26 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 155 THROUGH 222 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 223 THROUGH 272 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 273 THROUGH 381 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 382 THROUGH 500 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 1 THROUGH 15 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 16 THROUGH 18 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 19 THROUGH 26 )
16X-RAY DIFFRACTION16CHAIN 'F' AND (RESID 1 THROUGH 5 )
17X-RAY DIFFRACTION17CHAIN 'F' AND (RESID 6 THROUGH 10 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 11 THROUGH 15 )
19X-RAY DIFFRACTION19CHAIN 'F' AND (RESID 16 THROUGH 26 )

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