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- PDB-5okc: Crystal structure of the Ctf18-1-8 module from Ctf18-RFC -

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Basic information

Entry
Database: PDB / ID: 5okc
TitleCrystal structure of the Ctf18-1-8 module from Ctf18-RFC
Components
  • (Chromosome transmission fidelity protein ...) x 2
  • Sister chromatid cohesion protein DCC1
KeywordsREPLICATION / Clamp loader DNA-binding protein Triple beta-barrel domain Winged-helix domain
Function / homology
Function and homology information


maintenance of mitotic sister chromatid cohesion / Ctf18 RFC-like complex / telomere tethering at nuclear periphery / maintenance of DNA trinucleotide repeats / mitotic sister chromatid cohesion / nuclear replication fork / chromosome, centromeric region / DNA replication initiation / double-strand break repair via homologous recombination / DNA replication ...maintenance of mitotic sister chromatid cohesion / Ctf18 RFC-like complex / telomere tethering at nuclear periphery / maintenance of DNA trinucleotide repeats / mitotic sister chromatid cohesion / nuclear replication fork / chromosome, centromeric region / DNA replication initiation / double-strand break repair via homologous recombination / DNA replication / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Chromosome transmission fidelity protein 8 / Ctf8 / Sister chromatid cohesion protein Dcc1 / Sister chromatid cohesion protein Dcc1 / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NITRATE ION / Sister chromatid cohesion protein DCC1 / Chromosome transmission fidelity protein 8 / Chromosome transmission fidelity protein 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsGrabarczyk, D.B. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
CitationJournal: Structure / Year: 2018
Title: Structural Basis for the Recruitment of Ctf18-RFC to the Replisome.
Authors: Grabarczyk, D.B. / Silkenat, S. / Kisker, C.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sister chromatid cohesion protein DCC1
B: Sister chromatid cohesion protein DCC1
F: Chromosome transmission fidelity protein 8
G: Chromosome transmission fidelity protein 18
H: Chromosome transmission fidelity protein 8
I: Chromosome transmission fidelity protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,46513
Polymers127,0306
Non-polymers4347
Water6,792377
1
A: Sister chromatid cohesion protein DCC1
H: Chromosome transmission fidelity protein 8
I: Chromosome transmission fidelity protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7637
Polymers63,5153
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-41 kcal/mol
Surface area27540 Å2
MethodPISA
2
B: Sister chromatid cohesion protein DCC1
F: Chromosome transmission fidelity protein 8
G: Chromosome transmission fidelity protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7016
Polymers63,5153
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-47 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.515, 164.184, 59.613
Angle α, β, γ (deg.)90.000, 90.500, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain F
22chain H
13chain G
23chain I

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSERchain AAA2 - 3792 - 379
21SERSERARGARGchain BBB2 - 3802 - 380
12PROPROMSEMSEchain FFC2 - 1332 - 133
22PROPROMSEMSEchain HHE2 - 1332 - 133
13VALVALGLUGLUchain GGD137 - 1622 - 27
23THRTHRGLUGLUchain IIF136 - 1621 - 27

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sister chromatid cohesion protein DCC1 / Defective in sister chromatid cohesion protein 1


Mass: 44649.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: DCC1, YCL016C, YCL16C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25559

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Chromosome transmission fidelity protein ... , 2 types, 4 molecules FHGI

#2: Protein Chromosome transmission fidelity protein 8


Mass: 15564.851 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CTF8, YHR191C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38877
#3: Protein/peptide Chromosome transmission fidelity protein 18


Mass: 3300.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CTF18, CHL12, YMR078C, YM9582.03C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49956

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Non-polymers , 3 types, 384 molecules

#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 16% PEG 3350, 0.1 M HEPES pH 7.0, 0.2 M potassium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→48.24 Å / Num. obs: 49802 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.96 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.243 / Net I/σ(I): 6.9 / Num. measured all: 337988 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.3-2.386.92.36645700.4811100
9.2-48.246.30.118020.991199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
CRANK2phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.235 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.25
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 2460 4.95 %Random selection
Rwork0.2002 ---
obs0.2031 49746 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.8 Å2 / Biso mean: 55.2498 Å2 / Biso min: 20.37 Å2
Refinement stepCycle: final / Resolution: 2.3→48.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8605 0 28 377 9010
Biso mean--73.08 47.98 -
Num. residues----1059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028819
X-RAY DIFFRACTIONf_angle_d0.62911893
X-RAY DIFFRACTIONf_chiral_restr0.0251320
X-RAY DIFFRACTIONf_plane_restr0.0031512
X-RAY DIFFRACTIONf_dihedral_angle_d10.9543355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3382X-RAY DIFFRACTION8.682TORSIONAL
12B3382X-RAY DIFFRACTION8.682TORSIONAL
21F1144X-RAY DIFFRACTION8.682TORSIONAL
22H1144X-RAY DIFFRACTION8.682TORSIONAL
31G240X-RAY DIFFRACTION8.682TORSIONAL
32I240X-RAY DIFFRACTION8.682TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.34430.36581310.31826132744
2.3443-2.39210.34341220.308226442766
2.3921-2.44410.36581570.305126082765
2.4441-2.5010.33451350.287625912726
2.501-2.56350.3451070.280826732780
2.5635-2.63280.3641310.271326052736
2.6328-2.71030.29361040.260526742778
2.7103-2.79780.32471390.261526012740
2.7978-2.89780.31571390.253326242763
2.8978-3.01380.30531760.240325802756
3.0138-3.15090.30521180.215926382756
3.1509-3.3170.26551850.209625902775
3.317-3.52480.25211080.19326452753
3.5248-3.79680.25661480.176326172765
3.7968-4.17870.19991390.155826462785
4.1787-4.78290.19131510.143925992750
4.7829-6.02410.19081530.166226562809
6.0241-48.24580.25171170.159426822799
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)
11.1898-1.58390.2624.5331-0.94781.9276-00.15960.0985-0.1678-0.1323-0.0538-0.3320.05240.08370.4164-0.0517-0.01130.2319-0.01120.216269.3064-38.903263.9139
22.4535-0.09850.47692.51180.08322.5524-0.148-0.14560.31620.3416-0.0781-0.202-0.67160.4290.19990.663-0.1034-0.02860.38230.0050.259163.24161.182443.1931
33.5304-0.1148-2.13450.08950.18343.2515-0.090.0943-0.61830.1217-0.10150.17270.3906-0.49740.10060.583-0.11720.0160.3145-0.00370.416337.7408-7.65641.8415
40.556-0.9991-0.47244.98371.81331.4804-0.0120.1471-0.0599-0.0776-0.10810.0620.285-0.02540.11890.47340.0082-0.01030.29560.01590.261116.897744.385493.1346
52.4752-0.43950.43080.2591-0.16261.9938-0.05560.13120.18880.1451-0.0104-0.0256-0.20280.18450.04860.5286-0.02350.00080.1780.02370.26240.424518.469671.7273
63.28070.52930.79578.8857-1.61486.1301-0.15340.48910.4096-2.12360.2521.1488-0.2497-0.207-0.03740.5296-0.00910.02540.3854-0.01610.289610.96755.934184.2396
75.57381.4410.86581.2409-0.11712.1380.4098-0.5168-0.05020.2704-0.1119-0.2539-0.0916-0.0883-0.25170.5070.0233-0.03640.17880.00990.307611.660264.7344109.846
87.4129-0.14-2.29712.32131.52753.70570.37940.17810.55630.47240.0522-0.20670.01430.1435-0.40910.46670.0915-0.05760.17560.02690.355713.688969.5878104.6394
91.66561.53810.74096.94782.11353.108-0.20010.16650.304-0.0410.1932-0.4817-0.19810.0933-0.00560.30610.1015-0.01080.18750.01220.313920.094658.950197.4017
102.0226-1.29212.12356.0639-0.29964.13060.0544-0.80280.74630.57630.3764-0.31170.5066-0.7915-0.38180.40970.0347-0.08720.504-0.06440.462716.935267.0196116.5676
112.09752.51852.20563.53293.09652.7176-0.26510.10640.377-0.36560.15540.1036-0.21460.0484-0.0560.58050.1067-0.04420.2749-0.02980.480228.838650.0146106.1595
123.5025-1.24733.71862.4035-1.57153.97830.00130.6508-0.07621.12410.16621.2356-0.1061-0.7526-0.03870.44050.04720.09520.74920.02030.428213.20838.401799.1617
133.58810.0640.25628.03371.52524.2366-0.07260.3889-0.3121-1.4363-0.1548-1.29251.15510.17850.31930.916-0.01260.18950.37310.08740.31676.8482-36.064153.113
147.98672.141.72841.3223-1.86657.6495-0.52190.4438-1.0512-1.58280.1809-0.63561.89010.41940.36560.8531-0.03230.15690.38360.01410.46173.8559-50.766157.4042
156.3782-2.56540.06563.1913-1.48191.0711-0.3052-0.20920.82290.18470.02020.1705-0.36350.08210.21760.3312-0.04710.08980.20890.02540.368367.8217-48.390777.3749
165.57690.10060.361.4977-1.49484.22640.4505-0.5191-0.48590.6374-0.1802-0.29030.15740.3592-0.2190.5868-0.0372-0.0580.240.01530.245379.7324-56.084378.8254
174.9151-1.74051.34357.2018-5.01073.5313-0.07960.0506-0.13360.06080.19450.47140.1848-0.4973-0.18080.3483-0.01270.01030.20410.00320.272161.9848-58.628872.3066
189.49516.95017.33785.42315.99476.85630.4319-0.3922-0.08920.045-0.2046-0.2627-0.3876-0.3166-0.22070.5782-0.0083-0.0170.23330.03590.293466.9118-38.684561.2716
193.52722.8735-0.575.6144-1.02141.6063-0.12110.114-0.03610.09130.04670.04440.01320.06340.15630.44770.101-0.02390.21160.01340.197967.7125-46.21567.7559
203.9775-1.1635-1.70594.89243.88483.60680.0955-1.811-0.04480.38840.08650.4698-0.27220.2087-0.15210.5801-0.06070.06790.41330.16010.385164.8154-52.528384.9031
218.23835.6542-6.94474.6433-6.22248.7050.2816-0.1656-0.659-0.1086-0.3959-0.3021-0.07230.4955-0.02660.43590.031-0.00880.2732-0.02840.275263.9654-29.455670.4577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 122 )A2 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 227 )A123 - 227
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 379 )A228 - 379
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 146 )B2 - 146
5X-RAY DIFFRACTION5chain 'B' and (resid 147 through 380 )B147 - 380
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 27 )F2 - 27
7X-RAY DIFFRACTION7chain 'F' and (resid 28 through 58 )F28 - 58
8X-RAY DIFFRACTION8chain 'F' and (resid 59 through 87 )F59 - 87
9X-RAY DIFFRACTION9chain 'F' and (resid 88 through 133 )F88 - 133
10X-RAY DIFFRACTION10chain 'G' and (resid 137 through 141 )G137 - 141
11X-RAY DIFFRACTION11chain 'G' and (resid 142 through 156 )G142 - 156
12X-RAY DIFFRACTION12chain 'G' and (resid 157 through 162 )G157 - 162
13X-RAY DIFFRACTION13chain 'H' and (resid 2 through 16 )H2 - 16
14X-RAY DIFFRACTION14chain 'H' and (resid 17 through 30 )H17 - 30
15X-RAY DIFFRACTION15chain 'H' and (resid 31 through 44 )H31 - 44
16X-RAY DIFFRACTION16chain 'H' and (resid 45 through 76 )H45 - 76
17X-RAY DIFFRACTION17chain 'H' and (resid 77 through 96 )H77 - 96
18X-RAY DIFFRACTION18chain 'H' and (resid 97 through 106 )H97 - 106
19X-RAY DIFFRACTION19chain 'H' and (resid 107 through 133 )H107 - 133
20X-RAY DIFFRACTION20chain 'I' and (resid 136 through 145 )I136 - 145
21X-RAY DIFFRACTION21chain 'I' and (resid 146 through 162 )I146 - 162

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