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- PDB-5byg: X-ray structure of AAV2 OBD-AAVS1 complex 2:1 -

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Basic information

Entry
Database: PDB / ID: 5byg
TitleX-ray structure of AAV2 OBD-AAVS1 complex 2:1
Components
  • DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)-3')
  • DNA (5'-D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)-3')
  • Protein Rep78
KeywordsDNA Binding protein/DNA / Protein-DNA complex / DNA Binding protein-DNA complex
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / viral DNA genome replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication / host cell nucleus / ATP binding
Similarity search - Function
Rep protein catalytic-like / Rep protein catalytic domain like / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DNA / DNA (> 10) / Protein Rep78
Similarity search - Component
Biological speciesAdeno-associated virus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMusayev, F.N. / Escalante, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM09285 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1.
Authors: Musayev, F.N. / Zarate-Perez, F. / Bishop, C. / Burgner, J.W. / Escalante, C.R.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Aug 9, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Protein Rep78
B: Protein Rep78
C: Protein Rep78
D: Protein Rep78
E: DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)-3')
F: DNA (5'-D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)-3')
G: DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)-3')
H: DNA (5'-D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,44713
Polymers123,9908
Non-polymers4575
Water2,306128
1
A: Protein Rep78
B: Protein Rep78
E: DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)-3')
F: DNA (5'-D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2367
Polymers61,9954
Non-polymers2413
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-38 kcal/mol
Surface area25670 Å2
MethodPISA
2
C: Protein Rep78
D: Protein Rep78
G: DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)-3')
H: DNA (5'-D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2116
Polymers61,9954
Non-polymers2162
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-29 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.136, 79.595, 139.502
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein Rep78


Mass: 24551.828 Da / Num. of mol.: 4 / Fragment: UNP residues 1-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 2 / Strain: isolate Srivastava/1982 / Gene: Rep78 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: Q89268

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)-3')


Mass: 6343.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)-3')


Mass: 6548.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 133 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 4.32 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Per-6K, Sodium Citrate, Lithium Chloride / PH range: 5-5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2013
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 65724 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 18.7
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZO0
Resolution: 2.5→29.396 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 3316 5.06 %
Rwork0.1894 --
obs0.1914 65509 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 1710 29 128 7847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098069
X-RAY DIFFRACTIONf_angle_d1.11411323
X-RAY DIFFRACTIONf_dihedral_angle_d22.5433047
X-RAY DIFFRACTIONf_chiral_restr0.0461260
X-RAY DIFFRACTIONf_plane_restr0.0061162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.53580.3571950.31711932X-RAY DIFFRACTION72
2.5358-2.57370.33191120.30772231X-RAY DIFFRACTION82
2.5737-2.61390.29451230.30592310X-RAY DIFFRACTION85
2.6139-2.65670.33711340.30772344X-RAY DIFFRACTION87
2.6567-2.70250.33581270.30362487X-RAY DIFFRACTION91
2.7025-2.75160.37221370.29762545X-RAY DIFFRACTION94
2.7516-2.80450.28681420.29592577X-RAY DIFFRACTION96
2.8045-2.86170.33351480.29682639X-RAY DIFFRACTION97
2.8617-2.92380.36061400.29892671X-RAY DIFFRACTION98
2.9238-2.99180.35361340.2692645X-RAY DIFFRACTION98
2.9918-3.06650.26981360.24622705X-RAY DIFFRACTION98
3.0665-3.14930.29441410.23942680X-RAY DIFFRACTION98
3.1493-3.24190.32271260.22632669X-RAY DIFFRACTION98
3.2419-3.34640.27441320.22192688X-RAY DIFFRACTION98
3.3464-3.46580.22541390.21072685X-RAY DIFFRACTION98
3.4658-3.60440.20791490.20032677X-RAY DIFFRACTION99
3.6044-3.76810.23141440.20732701X-RAY DIFFRACTION99
3.7681-3.96630.20521540.17892698X-RAY DIFFRACTION99
3.9663-4.21410.21341630.15012676X-RAY DIFFRACTION99
4.2141-4.53840.19381500.13412716X-RAY DIFFRACTION99
4.5384-4.99310.17221280.13562739X-RAY DIFFRACTION99
4.9931-5.71110.19751370.14152731X-RAY DIFFRACTION99
5.7111-7.1780.1941590.16152741X-RAY DIFFRACTION99
7.178-29.39780.18551660.15732706X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.6821-3.3285-0.99984.4228-2.18986.65140.75570.0126-0.45270.38-0.50260.06151.3323-0.8923-0.36270.5188-0.2834-0.1170.6863-0.08350.55264.1872-57.9619191.3191
23.8625-4.028-5.5644.41995.9958.7344-0.17691.15932.0391-0.47630.44-0.774-1.25460.58230.08680.5308-0.1273-0.05340.51920.140.88011.9969-41.1176191.53
30.9232-1.72331.99443.7677-3.31034.1002-0.40350.58771.147-1.89421.08691.54630.85450.1051-0.38850.7467-0.1526-0.13931.3160.1731.0887-16.4253-43.5163182.6786
43.18613.9356-2.34075.9341-0.87588.29910.48640.20191.7407-0.85730.08441.6013-0.3477-1.3432-0.26910.68940.1111-0.02080.95730.20461.2731-19.1765-42.8791190.1002
58.5531-4.70160.91679.69896.51836.9040.57040.89072.0789-0.92710.4410.6773-2.2599-0.0741-0.95280.9983-0.0822-0.0220.54410.2861.2513-7.9485-37.9175185.0985
66.555-4.9725-2.71976.74282.91975.3135-0.36371.17450.8178-1.05410.5-0.5781-0.46220.1298-0.31790.7157-0.3762-0.06570.7140.02770.67344.8418-49.9189179.2288
73.3183-3.7994-4.11727.73665.90068.4519-0.04990.18260.3403-0.6320.22640.3911-0.6652-0.4374-0.12650.573-0.1032-0.07210.5671-0.03640.7342-3.9736-50.168188.4986
86.5541.77442.8398.372-3.8994.0831-0.3926-1.27850.38180.4136-0.185-0.2305-1.20870.78920.97530.6118-0.08860.161.0667-0.13070.9791-2.8125-39.3429195.7939
92.6518-0.86061.88391.1837-1.12081.804-0.2260.8978-0.06450.2820.4563-0.19640.4603-0.3457-0.09950.6035-0.2074-0.09410.3948-0.10080.62574.9388-55.7465187.701
108.0566-4.5901-0.22346.3683-2.08231.8287-0.29210.69210.8771-0.4428-0.0982-0.40070.04710.50060.09160.6037-0.4036-0.060.9277-0.14410.58115.2173-50.2495185.8576
118.1668-4.1381-7.43097.58890.49948.6866-0.15210.81781.8333-1.56320.0151-2.0228-1.76342.39250.2770.8568-0.36540.07620.8250.15551.04368.6975-38.8095179.3826
124.3309-2.3089-2.61416.4987-3.30215.7420.9823-0.28442.30210.1230.35740.7349-1.21880.9891-1.05290.9106-0.42860.2120.53730.26211.50016.5987-33.4136182.7711
132.92192.0037-2.31865.3796-4.85264.5220.457-1.01510.93341.24750.76140.8699-1.49970.4248-0.95991.0924-0.31660.10410.6568-0.16111.04687.1323-37.4034192.2111
145.43650.5553-1.43184.1538-2.2521.4741-0.0542-2.13630.41641.6295-0.5246-0.286-1.83251.49530.24170.731-0.2836-0.06311.0499-0.12690.648511.5643-50.2461200.7509
152.9113-3.5157-2.59686.03851.4584.0644-1.1131-0.4561-0.88070.39791.2277-0.2059-0.78021.64530.12110.4339-0.188-0.05510.7338-0.09830.618411.5631-54.6196197.7221
163.379-3.036-1.34173.1236-0.05966.5036-0.0873-0.04760.6530.5278-0.3349-0.6109-0.17941.38180.65260.4695-0.1409-0.08910.51970.05330.7338-3.3696-58.2593197.3052
174.96193.3726-1.87286.9034-3.39776.80550.41730.14050.59560.5580.36440.7189-1.0418-0.5771-0.7260.6017-0.0728-0.00010.4360.03270.7401-10.9365-47.2578193.389
185.1312-4.2062-4.03144.83392.82713.92-0.17571.3173-1.9524-1.3826-0.49341.62790.7402-0.29110.53210.5917-0.2557-0.12290.8584-0.06030.6843-7.9779-59.4939185.3855
198.52252.4974-2.02956.9344-0.36953.7973-0.26061.0356-0.99520.0522-0.00051.08640.2729-0.96990.27140.4759-0.12820.0040.83760.01920.6553-14.8675-59.1326194.8831
203.10170.9311.33694.4234-2.11964.0034-0.42530.9972-3.77331.55911.1982-0.98892.5756-0.3376-0.14060.8325-0.00350.18710.64310.11121.2668-8.4136-71.7308205.5015
211.5788-0.80920.17893.083-2.88475.4887-0.42460.95120.68140.99340.03680.4661-0.90130.14020.28520.4629-0.1558-0.07520.7612-0.02880.723740.0705-32.4361188.1032
225.4591-4.43-0.09214.0182-1.74448.0995-0.26581.0836-0.7020.21840.4097-1.3670.81890.97780.41010.509-0.0670.0310.8097-0.28120.966855.6456-44.4379189.588
234.3256-2.6298-1.57661.6955-0.26559.8960.7214-0.9877-0.6839-0.49210.30830.9798-0.30740.35770.27150.6281-0.12690.14170.97380.10441.071772.4088-46.0585180.8413
242.12971.80531.54594.46964.44324.3841-1.27840.5705-0.07160.63041.25750.497-0.72692.0233-0.0980.7926-0.1950.0410.98080.00630.867268.7107-34.7056183.3115
253.88483.8329-3.72693.7446-3.63183.6019-0.3779-0.32450.14940.31630.1743-0.5254-0.546-0.23130.39990.4652-0.1805-0.04710.7632-0.18440.789964.8226-23.915194.7183
264.0344-1.8375-1.24144.877-1.07915.3113-0.17690.763-0.442-0.55490.107-0.44370.66110.56860.02110.5014-0.2210.14790.697-0.13030.656756.9591-35.7133183.0953
274.76591.02244.94665.7783.13489.17940.59411.53640.6653-0.7137-0.0692-0.6029-0.4021-0.6790.23370.7215-0.2022-0.09931.05640.06730.722442.4335-29.4586174.3061
282.6005-0.6713.07575.3143-1.6477.4431-0.7683-0.6410.602-0.48320.2988-0.41370.9284-1.22350.39570.4614-0.10670.12870.7013-0.0260.628752.3168-33.0231190.488
293.93393.0394-4.29463.3444-1.86147.60290.67820.5495-1.60711.7651-0.59330.51711.0654-1.52860.00370.9942-0.3919-0.10531.2015-0.07991.133556.7348-44.5092195.7865
304.9841-4.55594.55025.8275-4.76254.35531.0937-1.84690.2282-0.83740.29440.03481.6203-0.684-1.10980.4737-0.22140.010.7293-0.20370.632248.233-35.5853188.7185
312.619-2.5618-3.45753.18474.13855.3476-0.63871.38630.0286-0.97170.6086-0.00810.0435-1.19790.06660.5863-0.3293-0.07970.96620.03840.696335.9957-36.6787180.1568
323.92530.34874.23920.08530.38944.53220.4251.3682-1.8143-0.49990.02160.09531.48230.4914-0.73610.7704-0.36330.12720.959-0.30490.881945.8918-44.3794176.6878
336.5332-4.6518-1.72484.53033.16564.51440.04712.9742-1.3895-0.8873-0.3193-0.28651.2129-0.18180.12240.6825-0.25570.09021.1443-0.39551.173758.3257-47.1881176.5977
342.6848-1.164-0.55936.0072-1.54993.299-0.2114-0.2113-0.2426-0.2615-0.0749-0.34220.3939-0.32010.16090.566-0.29330.05520.9631-0.13720.779142.5606-45.0298189.8339
355.30436.52944.86458.20065.50275.3349-0.6576-0.92480.01910.3238-0.12480.2640.02-2.25710.55010.5266-0.16790.05341.0334-0.17810.677145.3559-29.3805197.6947
369.2858-1.45110.41023.2078-1.66655.6437-0.34-0.21750.0702-0.15950.0488-0.08420.12640.09370.1770.4707-0.18450.05590.6184-0.12870.70255.6744-29.632193.3664
379.2419-1.64471.17273.6718-2.09876.1529-0.38290.22910.74230.2710.17610.0877-1.0619-0.09250.15760.5135-0.1027-0.02550.605-0.11660.679253.9681-22.3872195.3011
387.8373-1.7339-8.43677.19580.76919.2602-0.88130.15181.1481-0.3950.3321-0.1055-0.3456-1.76670.52450.5565-0.0759-0.10530.8742-0.20060.661146.6176-21.134203.4056
392.9418-4.9887-3.12178.80245.59343.56940.6137-0.46231.3735-0.7143-0.3616-0.5338-0.0934-0.4572-0.56720.62050.0508-0.07350.6664-0.11420.819736.2806-22.0808207.2421
405.2875-4.152-5.72887.03092.15947.8685-0.22880.44951.5234-0.82070.2622.5590.3378-1.2639-0.17880.74520.0455-0.0471.0984-0.10681.135226.9439-22.6697211.3202
416.54310.2932-4.30012.49461.00163.59040.56780.08561.0510.2811-1.2189-0.0249-0.30240.50270.89690.5875-0.29920.01391.1745-0.08990.70426.382810.0676164.8132
422.8211-1.78383.1881.5164-2.02273.59970.4666-0.58560.0826-0.6431-0.10021.07560.25220.12820.97060.6633-0.21920.0680.9726-0.32250.9009-10.6098-0.0835162.5523
433.1587-4.3037-4.4065.86646.00536.610.08712.2333-0.5707-2.19970.4619-0.60710.22410.1489-0.1590.9711-0.38850.25081.5933-0.44261.1498-28.2624-4.7277169.6323
446.36844.17635.11549.19670.65377.191-0.2942.7870.0985-0.05680.46430.3757-0.5473-0.229-0.02580.6275-0.28340.18591.238-0.20590.7823-23.73163.5203171.6172
459.29330.6914-3.02942.0682-1.44575.99420.31940.6957-0.15530.97290.15810.4256-1.2201-0.5432-0.34880.79520.08220.02280.96510.03170.8403-19.934218.9319168.3458
464.8498-5.2884-2.57669.1294-0.13444.00720.28782.21240.7647-0.836-0.261.1625-0.2883-1.5435-0.06680.54210.0392-0.11471.46280.17730.6813-21.009217.3965159.6071
476.0095-5.3092-0.01287.1686-3.40184.7047-0.41351.3918-0.0591-0.02530.52540.90270.9147-1.56720.25020.5569-0.25380.0821.0348-0.13240.8616-20.04566.3637164.3434
487.5476-3.26136.34436.9903-6.24837.5314-1.0936-0.09341.580.67430.03480.23130.6749-0.77961.11580.5436-0.13750.11240.676-0.20140.6124-11.94595.3741171.156
495.4919-2.2189-0.81243.7891-2.41453.2742-0.14160.8903-0.0836-0.163-0.0923-0.20880.03250.76280.1350.5933-0.14690.00690.7637-0.1650.3905-3.3087.0027169.6437
504.3230.7045-0.49655.5411-1.42544.444-0.2062.18550.7716-0.0430.06180.57390.1278-0.16890.08160.4273-0.08150.01850.9164-0.19970.4849-3.33067.3375163.4785
513.9073-4.6209-0.42826.0031-1.0643.6339-0.54690.0562-0.20740.7880.2322-0.3170.08820.49280.34890.5837-0.0068-0.00260.9747-0.15970.45668.1186-0.7042171.0933
525.69944.364.30863.7133.01433.66480.03860.9241-3.2196-0.7051-0.2457-1.17761.31290.38730.46140.6944-0.10080.16450.9222-0.17530.8299-4.925-5.3612172.1143
536.26455.30911.92944.48491.57211.42490.2198-1.3336-1.86330.38540.0225-0.73220.8462-1.1853-0.29360.7231-0.28250.1140.9182-0.13750.9422-12.9176-6.9211172.9245
543.35320.7541-1.8445.4842-3.84723.2077-0.81640.359-1.0697-1.2960.79690.40632.3686-0.02450.0021.0477-0.21280.07311.2175-0.35630.7993-8.7511-8.2542160.9878
552.3238-1.3674-2.93084.48932.36473.8951-0.39881.21230.7883-0.66360.20640.52191.44630.45050.36840.7489-0.05370.08331.2058-0.25460.60252.4853-1.406158.6086
563.23751.9570.61371.3881.38937.7851-0.3511.6136-0.1263-0.5920.1321.09390.6912-0.1554-0.10880.5749-0.10290.0761.2234-0.16890.66918.98671.8316158.612
574.764-5.06324.35965.3211-4.57893.9310.09022.209-0.0682-0.7216-0.4739-0.9279-0.70811.25050.61340.7108-0.2380.09541.37720.17140.59390.804116.0446157.4838
588.92190.572-0.51116.2456-2.06669.0194-0.45571.13110.2023-0.61390.18940.246-0.4434-1.50370.02590.5454-0.14350.01520.9190.02750.4776-10.135515.2651161.5688
595.0882-2.5966-0.77888.13191.08334.15950.05620.68881.1293-0.3063-0.0548-0.0615-0.8565-0.02850.17090.7347-0.1261-0.00760.89470.08980.5363-8.570122.7622161.6767
604.7665-0.8208-4.79520.09740.88555.00280.42830.88481.14390.23050.3976-0.7447-1.1873-0.6236-0.50971.0706-0.24730.01451.15450.33420.97463.348927.3382153.4161
617.6477-0.5662-1.78174.4968-2.15853.60131.0971-2.8904-0.52-1.9131-1.6687-3.1373-0.1163.8178-0.49310.73790.38370.1351.8254-0.19850.877535.9722-11.703147.835
623.8417-3.67982.85824.8896-0.19656.66790.92021.38752.34660.4522-0.4607-1.50621.02252.8612-0.67360.84930.26170.11091.5346-0.22491.415356.7576-4.2314148.9515
634.8545-1.80883.00411.2888-0.93371.89-0.04490.45012.1341-0.3835-0.35850.0584-0.54320.50010.8618-0.8627-1.1193-0.05022.9512-1.62052.389755.87584.888149.7417
640.0706-0.1570.25090.3885-0.54660.7759-0.374-1.07451.50480.4541.1916-1.3359-1.27671.3749-0.19261.0422-0.332-0.03872.4736-1.11211.313144.6228-3.3162157.8976
653.4463-3.1106-4.06254.81823.81924.8078-0.6525-1.28260.11712.83641.1356-0.23420.31541.115-0.51861.20190.2874-0.15942.233-0.2710.795638.2062-12.8603160.7663
668.1326.0589-7.32115.9765-7.16339.3747-0.7707-1.21530.4256-0.69610.7108-1.41920.96763.002-0.60050.81130.1470.07142.1975-0.4770.885445.2919-12.9907152.0997
674.62223.4421.74444.81490.6390.84220.3681-1.1470.6272-2.45870.2181-2.0578-0.0909-0.161-0.16951.0642-0.30160.42481.6664-0.421.629846.59672.4432143.3781
686.89220.0432.84523.6588-0.85375.1612-1.3830.49790.8709-2.26040.0275-0.52051.09270.75431.25881.2593-0.45940.43212.1898-0.53811.670643.45443.5992146.3003
692.7723-1.9787-3.3431.16562.18939.3329-0.2086-0.74130.38710.20370.6749-0.2480.67051.2094-0.35370.80220.15020.0891.407-0.32860.808732.2027-10.6375154.4421
703.8953-2.6613-2.89423.58931.78732.83540.9662-1.44041.24252.24780.03960.4461-0.9060.1649-0.3191.04270.18460.11081.824-0.52211.173634.65321.0565161.4024
714.69251.6727-1.51033.47994.30878.58881.2167-2.4621.46731.73620.0416-1.1204-1.45410.446-0.25111.4696-0.1691-0.11281.8455-0.62451.208638.96365.9749162.8239
722.19521.5475-2.56354.2727-4.385.1775-0.2166-0.82741.0407-1.19421.46790.1355-0.81520.5229-0.98481.2226-0.073-0.03571.3036-0.60931.645734.96485.5649151.3767
736.4256-2.23915.26646.27360.77625.8365-1.13220.93340.5466-0.8161-0.1472-0.6404-0.9161-1.17050.29971.01660.05340.29181.5995-0.30670.83928.8406-4.4785142.3248
748.4863-4.427-0.61769.18461.85783.46720.22011.0724-0.5415-0.64930.2933-0.44960.03980.5495-0.31170.8250.00490.10061.5984-0.29310.754434.555-11.9771142.4868
752.109-0.21092.60330.0212-0.26493.20740.23930.09050.2501-0.55330.5439-0.2698-0.20652.99940.00290.69010.13120.56162.6829-0.90981.008645.1882-10.3825138.3494
764.0779-5.5603-2.78977.74474.54395.87250.98-0.66552.17911.02420.2868-0.54360.0360.18-0.34480.8069-0.3080.55272.0534-0.60261.771752.8457-2.4859138.5017
775.42235.6113-4.1196.1809-4.20554.03681.37280.14891.50740.34080.60210.135-1.46611.9909-1.52851.1939-0.32590.38892.7893-0.93871.533151.913-2.113147.1208
784.52381.4685.07042.21911.12255.92960.13840.34890.12650.82590.6718-1.51431.61163.5894-0.62131.05980.2574-0.24542.1332-0.56791.257751.8652-15.8764148.4207
791.6121-1.4036-0.92448.30056.19434.64541.388-2.53420.46030.1645-0.4538-5.20480.20812.4951-0.04940.77070.00240.04832.7-0.50772.064358.1153-9.1958142.3882
806.92890.3219-0.73893.18774.32599.33890.3113-1.61210.50850.4644-0.58990.08010.9544-0.22120.09041.00150.31960.26981.82-0.04010.888646.9787-20.4948129.0102
814.6291.58764.29929.4190.08954.1547-0.34383.2398-1.7442-2.33680.4447-0.42731.89610.21690.29771.8776-0.19840.1411.5619-0.06690.812417.2106-56.1307222.5993
829.7832-3.3022-1.89727.31884.0834.4410.352-3.22240.82340.93510.00220.3938-0.36051.7415-0.39170.977-0.30450.01531.7786-0.12370.754118.4313-47.84209.7039
838.0728-4.5617-2.18053.11652.89385.86341.0754-0.52520.52480.9339-0.7073-1.4643-0.04440.7897-0.38970.6693-0.322-0.03271.41320.01550.870330.1223-52.9987198.8765
843.99341.3906-2.7759.5891-6.05044.80420.27110.5144-0.1725-0.1852-0.8497-0.40830.01911.37980.66190.6219-0.2598-0.00210.9821-0.13710.629624.4497-54.4431183.3786
855.34475.4718-3.99668.6299-4.99037.6806-0.88542.0856-0.845-1.49910.2808-0.36261.1098-0.45270.75710.9487-0.46290.05111.5979-0.16330.675432.9493-45.4512170.2357
865.2237-4.17443.35245.1995-4.75844.58430.86183.5632-0.6055-0.24190.30072.32490.1071-1.3347-0.68151.2246-0.57870.03472.5221-0.0820.942328.2942-50.8198163.4913
876.5776-6.17212.06267.67131.74947.1644-0.28030.3515-0.5531-0.77010.5527-0.26540.7279-0.7574-0.21020.6998-0.28330.07391.1471-0.11110.750633.9728-51.3057177.9509
885.46945.5864-3.4836.7708-3.41932.0899-0.0481-0.68450.8583-0.12080.70290.0609-0.54711.705-0.62060.6088-0.3820.02151.142-0.09880.750824.4219-48.1798190.193
892.0422-0.33922.8397.03662.48817.49430.1343-1.9602-0.42281.35790.0986-0.1017-0.67130.6283-0.28470.7823-0.3051-0.06451.34020.1060.722922.8296-56.5211203.8465
904.005-0.14663.71762.58041.07644.4676-0.2858-1.45151.20872.01580.9991-0.2028-0.02452.4369-0.71121.3262-0.22170.10951.7094-0.08880.893220.8191-47.8906218.7863
918.20480.06591.95087.22171.50535.64920.2223-2.9291-0.15691.28260.5696-0.68420.7607-1.158-0.50371.69430.42210.09192.10710.04390.809421.0608-9.0032124.4136
924.18922.90774.27132.45022.75054.476-0.803-1.33580.2013-0.76150.3863-0.05130.22773.12560.59541.27410.17210.22421.8804-0.08260.958916.9354-0.6545138.0065
937.9045-1.92681.7724.8698-0.43114.17610.4836-0.3956-0.1658-0.2290.02460.71870.6555-1.2181-0.39240.7996-0.19240.22231.6851-0.32620.850812.0213-10.9383150.1418
941.9873-0.8842-1.56673.18160.58874.1157-0.6575-0.9286-0.00660.02890.1003-0.17630.67180.82450.45460.81820.16740.09071.5657-0.14580.748320.7318-10.9897164.2715
952.1119-1.0435-2.63765.9582-0.88065.84990.3756-1.5029-0.71041.0505-0.0773-0.32290.90181.9216-0.58610.88540.106-0.03751.2252-0.07110.626611.9776-7.959178.1573
969.2571-2.4784-1.6059.63673.56575.305-0.3336-1.4419-1.24510.78231.5426-0.64220.34552.1524-1.12321.18630.36270.16621.6014-0.15310.862317.1886-14.885179.3586
973.36571.3598-2.76046.4676-5.82555.74080.19550.1943-0.3673-0.8972-0.32610.13840.89341.39830.21220.6944-0.01740.04921.2404-0.17320.610811.9783-8.2006164.8349
986.2218-5.1058-3.90741.99996.32254.02081.01241.6508-0.35810.2872-0.0698-0.56030.0341-0.7246-0.72940.92620.09070.24281.5288-0.22080.820320.2049-6.6401151.4171
997.07093.61393.0453.68890.1142.56470.00732.6443-0.0647-1.75371.56260.20910.8294-0.4026-0.95961.2268-0.01480.03172.2031-0.22050.812114.4531-9.9473136.6566
1008.74284.6958-5.12239.6244-6.21885.76461.41160.19261.69680.12390.8627-0.1495-1.02291.0077-2.14782.13390.51260.14332.4704-0.20131.073917.7416-0.7296123.9342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:6)
2X-RAY DIFFRACTION2(chain A and resid 7:12)
3X-RAY DIFFRACTION3(chain A and resid 13:40)
4X-RAY DIFFRACTION4(chain A and resid 41:48)
5X-RAY DIFFRACTION5(chain A and resid 49:57)
6X-RAY DIFFRACTION6(chain A and resid 58:74)
7X-RAY DIFFRACTION7(chain A and resid 75:85)
8X-RAY DIFFRACTION8(chain A and resid 86:91)
9X-RAY DIFFRACTION9(chain A and resid 92:100)
10X-RAY DIFFRACTION10(chain A and resid 101:113)
11X-RAY DIFFRACTION11(chain A and resid 114:119)
12X-RAY DIFFRACTION12(chain A and resid 120:125)
13X-RAY DIFFRACTION13(chain A and resid 126:133)
14X-RAY DIFFRACTION14(chain A and resid 134:140)
15X-RAY DIFFRACTION15(chain A and resid 141:148)
16X-RAY DIFFRACTION16(chain A and resid 149:156)
17X-RAY DIFFRACTION17(chain A and resid 157:169)
18X-RAY DIFFRACTION18(chain A and resid 170:176)
19X-RAY DIFFRACTION19(chain A and resid 177:195)
20X-RAY DIFFRACTION20(chain A and resid 196:201)
21X-RAY DIFFRACTION21(chain B and resid 1:7)
22X-RAY DIFFRACTION22(chain B and resid 8:13)
23X-RAY DIFFRACTION23(chain B and resid 14:28)
24X-RAY DIFFRACTION24(chain B and resid 29:36)
25X-RAY DIFFRACTION25(chain B and resid 37:45)
26X-RAY DIFFRACTION26(chain B and resid 46:69)
27X-RAY DIFFRACTION27(chain B and resid 70:75)
28X-RAY DIFFRACTION28(chain B and resid 76:85)
29X-RAY DIFFRACTION29(chain B and resid 86:90)
30X-RAY DIFFRACTION30(chain B and resid 91:95)
31X-RAY DIFFRACTION31(chain B and resid 96:106)
32X-RAY DIFFRACTION32(chain B and resid 107:116)
33X-RAY DIFFRACTION33(chain B and resid 117:124)
34X-RAY DIFFRACTION34(chain B and resid 125:149)
35X-RAY DIFFRACTION35(chain B and resid 150:159)
36X-RAY DIFFRACTION36(chain B and resid 160:173)
37X-RAY DIFFRACTION37(chain B and resid 174:185)
38X-RAY DIFFRACTION38(chain B and resid 186:194)
39X-RAY DIFFRACTION39(chain B and resid 195:200)
40X-RAY DIFFRACTION40(chain B and resid 201:207)
41X-RAY DIFFRACTION41(chain C and resid 1:6)
42X-RAY DIFFRACTION42(chain C and resid 7:21)
43X-RAY DIFFRACTION43(chain C and resid 22:27)
44X-RAY DIFFRACTION44(chain C and resid 28:34)
45X-RAY DIFFRACTION45(chain C and resid 35:40)
46X-RAY DIFFRACTION46(chain C and resid 41:48)
47X-RAY DIFFRACTION47(chain C and resid 49:54)
48X-RAY DIFFRACTION48(chain C and resid 55:61)
49X-RAY DIFFRACTION49(chain C and resid 62:88)
50X-RAY DIFFRACTION50(chain C and resid 89:97)
51X-RAY DIFFRACTION51(chain C and resid 98:111)
52X-RAY DIFFRACTION52(chain C and resid 112:117)
53X-RAY DIFFRACTION53(chain C and resid 118:124)
54X-RAY DIFFRACTION54(chain C and resid 125:130)
55X-RAY DIFFRACTION55(chain C and resid 131:139)
56X-RAY DIFFRACTION56(chain C and resid 140:148)
57X-RAY DIFFRACTION57(chain C and resid 149:158)
58X-RAY DIFFRACTION58(chain C and resid 159:173)
59X-RAY DIFFRACTION59(chain C and resid 174:186)
60X-RAY DIFFRACTION60(chain C and resid 187:200)
61X-RAY DIFFRACTION61(chain D and resid 1:8)
62X-RAY DIFFRACTION62(chain D and resid 9:42)
63X-RAY DIFFRACTION63(chain D and resid 43:55)
64X-RAY DIFFRACTION64(chain D and resid 56:63)
65X-RAY DIFFRACTION65(chain D and resid 64:74)
66X-RAY DIFFRACTION66(chain D and resid 75:80)
67X-RAY DIFFRACTION67(chain D and resid 81:87)
68X-RAY DIFFRACTION68(chain D and resid 88:91)
69X-RAY DIFFRACTION69(chain D and resid 92:112)
70X-RAY DIFFRACTION70(chain D and resid 113:117)
71X-RAY DIFFRACTION71(chain D and resid 118:126)
72X-RAY DIFFRACTION72(chain D and resid 127:132)
73X-RAY DIFFRACTION73(chain D and resid 133:140)
74X-RAY DIFFRACTION74(chain D and resid 141:152)
75X-RAY DIFFRACTION75(chain D and resid 153:157)
76X-RAY DIFFRACTION76(chain D and resid 158:163)
77X-RAY DIFFRACTION77(chain D and resid 164:169)
78X-RAY DIFFRACTION78(chain D and resid 170:178)
79X-RAY DIFFRACTION79(chain D and resid 179:184)
80X-RAY DIFFRACTION80(chain D and resid 185:207)
81X-RAY DIFFRACTION81(chain E and resid 1:4)
82X-RAY DIFFRACTION82(chain E and resid 5:8)
83X-RAY DIFFRACTION83(chain E and resid 9:12)
84X-RAY DIFFRACTION84(chain E and resid 13:16)
85X-RAY DIFFRACTION85(chain E and resid 17:21)
86X-RAY DIFFRACTION86(chain F and resid 22:25)
87X-RAY DIFFRACTION87(chain F and resid 26:29)
88X-RAY DIFFRACTION88(chain F and resid 30:33)
89X-RAY DIFFRACTION89(chain F and resid 34:37)
90X-RAY DIFFRACTION90(chain F and resid 38:42)
91X-RAY DIFFRACTION91(chain G and resid 1:5)
92X-RAY DIFFRACTION92(chain G and resid 6:9)
93X-RAY DIFFRACTION93(chain G and resid 10:13)
94X-RAY DIFFRACTION94(chain G and resid 14:17)
95X-RAY DIFFRACTION95(chain G and resid 18:21)
96X-RAY DIFFRACTION96(chain H and resid 22:26)
97X-RAY DIFFRACTION97(chain H and resid 27:30)
98X-RAY DIFFRACTION98(chain H and resid 31:34)
99X-RAY DIFFRACTION99(chain H and resid 35:38)
100X-RAY DIFFRACTION100(chain H and resid 39:42)

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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