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- PDB-3zwo: Crystal structure of ADP ribosyl cyclase complexed with reaction ... -

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Basic information

Entry
Database: PDB / ID: 3zwo
TitleCrystal structure of ADP ribosyl cyclase complexed with reaction intermediate
ComponentsADP-RIBOSYL CYCLASE
KeywordsHYDROLASE / CD38 / HYDROLYSIS / NAD / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / NAD+ nucleosidase activity, cyclic ADP-ribose generating / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / single fertilization / positive regulation of B cell proliferation / transferase activity / cytoplasmic vesicle / plasma membrane
Similarity search - Function
ADP Ribosyl Cyclase; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE DIPHOSPHATE RIBOSE / Chem-NGD / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKotaka, M. / Graeff, R. / Zhang, L.H. / Lee, H.C. / Hao, Q.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase.
Authors: Kotaka, M. / Graeff, R. / Chen, Z. / Zhang, L.H. / Lee, H.C. / Hao, Q.
History
DepositionAug 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Jan 25, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-RIBOSYL CYCLASE
B: ADP-RIBOSYL CYCLASE
C: ADP-RIBOSYL CYCLASE
D: ADP-RIBOSYL CYCLASE
E: ADP-RIBOSYL CYCLASE
F: ADP-RIBOSYL CYCLASE
G: ADP-RIBOSYL CYCLASE
H: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,24515
Polymers237,2088
Non-polymers4,0367
Water23,9241328
1
E: ADP-RIBOSYL CYCLASE
H: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4214
Polymers59,3022
Non-polymers1,1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-22.8 kcal/mol
Surface area23280 Å2
MethodPISA
2
B: ADP-RIBOSYL CYCLASE
G: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4214
Polymers59,3022
Non-polymers1,1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-21.4 kcal/mol
Surface area23190 Å2
MethodPISA
3
A: ADP-RIBOSYL CYCLASE
D: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8613
Polymers59,3022
Non-polymers5591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-12.7 kcal/mol
Surface area23240 Å2
MethodPISA
4
C: ADP-RIBOSYL CYCLASE
F: ADP-RIBOSYL CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5424
Polymers59,3022
Non-polymers1,2402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-16.9 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 76.422, 139.710
Angle α, β, γ (deg.)87.80, 89.09, 89.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEUAA6 - 247 - 25
21GLUGLULEULEUBB6 - 247 - 25
31GLUGLULEULEUCC6 - 247 - 25
41GLUGLULEULEUDD6 - 247 - 25
51GLUGLULEULEUEE6 - 247 - 25
61GLUGLULEULEUFF6 - 247 - 25
71GLUGLULEULEUGG6 - 247 - 25
81GLUGLULEULEUHH6 - 247 - 25
12CYSCYSPHEPHEAA34 - 4535 - 46
22CYSCYSPHEPHEBB34 - 4535 - 46
32CYSCYSPHEPHECC34 - 4535 - 46
42CYSCYSPHEPHEDD34 - 4535 - 46
52CYSCYSPHEPHEEE34 - 4535 - 46
62CYSCYSPHEPHEFF34 - 4535 - 46
72CYSCYSPHEPHEGG34 - 4535 - 46
82CYSCYSPHEPHEHH34 - 4535 - 46
13SERSERSERSERAA57 - 6458 - 65
23SERSERSERSERBB57 - 6458 - 65
33SERSERSERSERCC57 - 6458 - 65
43SERSERSERSERDD57 - 6458 - 65
53SERSERSERSEREE57 - 6458 - 65
63SERSERSERSERFF57 - 6458 - 65
73SERSERSERSERGG57 - 6458 - 65
83SERSERSERSERHH57 - 6458 - 65
14GLNGLNSERSERAA67 - 7868 - 79
24GLNGLNSERSERBB67 - 7868 - 79
34GLNGLNSERSERCC67 - 7868 - 79
44GLNGLNSERSERDD67 - 7868 - 79
54GLNGLNSERSEREE67 - 7868 - 79
64GLNGLNSERSERFF67 - 7868 - 79
74GLNGLNSERSERGG67 - 7868 - 79
84GLNGLNSERSERHH67 - 7868 - 79
15TYRTYRTHRTHRAA81 - 9082 - 91
25TYRTYRTHRTHRBB81 - 9082 - 91
35TYRTYRTHRTHRCC81 - 9082 - 91
45TYRTYRTHRTHRDD81 - 9082 - 91
55TYRTYRTHRTHREE81 - 9082 - 91
65TYRTYRTHRTHRFF81 - 9082 - 91
75TYRTYRTHRTHRGG81 - 9082 - 91
85TYRTYRTHRTHRHH81 - 9082 - 91
16LYSLYSLEULEUAA93 - 9794 - 98
26LYSLYSLEULEUBB93 - 9794 - 98
36LYSLYSLEULEUCC93 - 9794 - 98
46LYSLYSLEULEUDD93 - 9794 - 98
56LYSLYSLEULEUEE93 - 9794 - 98
66LYSLYSLEULEUFF93 - 9794 - 98
76LYSLYSLEULEUGG93 - 9794 - 98
86LYSLYSLEULEUHH93 - 9794 - 98
17LEULEUGLYGLYAA101 - 113102 - 114
27LEULEUGLYGLYBB101 - 113102 - 114
37LEULEUGLYGLYCC101 - 113102 - 114
47LEULEUGLYGLYDD101 - 113102 - 114
57LEULEUGLYGLYEE101 - 113102 - 114
67LEULEUGLYGLYFF101 - 113102 - 114
77LEULEUGLYGLYGG101 - 113102 - 114
87LEULEUGLYGLYHH101 - 113102 - 114
18PHEPHEASPASPAA139 - 160140 - 161
28PHEPHEASPASPBB139 - 160140 - 161
38PHEPHEASPASPCC139 - 160140 - 161
48PHEPHEASPASPDD139 - 160140 - 161
58PHEPHEASPASPEE139 - 160140 - 161
68PHEPHEASPASPFF139 - 160140 - 161
78PHEPHEASPASPGG139 - 160140 - 161
88PHEPHEASPASPHH139 - 160140 - 161
19ARGARGLEULEUAA189 - 195190 - 196
29ARGARGLEULEUBB189 - 195190 - 196
39ARGARGLEULEUCC189 - 195190 - 196
49ARGARGLEULEUDD189 - 195190 - 196
59ARGARGLEULEUEE189 - 195190 - 196
69ARGARGLEULEUFF189 - 195190 - 196
79ARGARGLEULEUGG189 - 195190 - 196
89ARGARGLEULEUHH189 - 195190 - 196
110GLYGLYALAALAAA209 - 220210 - 221
210GLYGLYALAALABB209 - 220210 - 221
310GLYGLYALAALACC209 - 220210 - 221
410GLYGLYALAALADD209 - 220210 - 221
510GLYGLYALAALAEE209 - 220210 - 221
610GLYGLYALAALAFF209 - 220210 - 221
710GLYGLYALAALAGG209 - 220210 - 221
810GLYGLYALAALAHH209 - 220210 - 221
111PHEPHEASPASPAA223 - 241224 - 242
211PHEPHEASPASPBB223 - 241224 - 242
311PHEPHEASPASPCC223 - 241224 - 242
411PHEPHEASPASPDD223 - 241224 - 242
511PHEPHEASPASPEE223 - 241224 - 242
611PHEPHEASPASPFF223 - 241224 - 242
711PHEPHEASPASPGG223 - 241224 - 242
811PHEPHEASPASPHH223 - 241224 - 242

NCS oper:
IDCodeMatrixVector
1given(0.5052, 0.6453, -0.573), (-0.6557, 0.7187, 0.2313), (0.5611, 0.2589, 0.7863)66.3287, -2.6419, -35.8916
2given(0.9999, 0.0137, 0.0059), (0.0135, -0.9994, 0.0315), (0.0063, -0.0314, -0.9995)28.683, -24.9904, 39.3886
3given(0.5975, 0.3021, 0.7428), (0.2732, -0.9476, 0.1656), (0.7539, 0.104, -0.6487)-14.5367, 9.5143, 27.3022
4given(0.4987, -0.666, 0.5548), (-0.6626, -0.7056, -0.2513), (0.5588, -0.2423, -0.7931)13.5771, 8.2861, -26.6063
5given(0.6015, -0.3145, -0.7343), (0.2847, 0.9433, -0.1707), (0.7464, -0.1064, 0.657)24.3101, 47.7116, 19.6667
6given(0.547, 0.7749, 0.3167), (0.8353, -0.4802, -0.2677), (-0.0553, 0.411, -0.91)-2.8619, 25.4176, 100.2408
7given(0.5373, -0.7739, -0.3353), (0.8413, 0.4635, 0.2782), (-0.0599, -0.4315, 0.9001)-24.1045, 2.1849, 55.5966

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Components

#1: Protein
ADP-RIBOSYL CYCLASE / ADRC / NAD GLYCOHYDROLASE / NAD(+) NUCLEOSIDASE / NADASE


Mass: 29651.023 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P29241, NAD+ glycohydrolase
#2: Chemical
ChemComp-G2Q / GUANOSINE DIPHOSPHATE RIBOSE


Mass: 559.316 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-NGD / 3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]PYRIDINIUM / NICOTINAMIDE GUANINE DINUCLEOTIDE


Mass: 680.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE ADDITIONAL ALANINE AT THE N-TERMINUS ARE ACTUALLY AMINO ACIDS LEFT OVER FROM THE CLEAVAGE OF ...THE ADDITIONAL ALANINE AT THE N-TERMINUS ARE ACTUALLY AMINO ACIDS LEFT OVER FROM THE CLEAVAGE OF THE SECRETORY SIGNALLING PROTEIN FOR SECRETION DURING EXPRESSION FROM PICHIA.

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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: 2.83 Å3/Da / Density % sol: 56.51 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M IMIDAZOLE, PH 7.5, 12-14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 163820 / % possible obs: 97.4 % / Observed criterion σ(I): 1.5 / Redundancy: 2.5 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R12

1r12


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.413 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22779 8220 5 %RANDOM
Rwork0.17691 ---
obs0.17941 155498 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.239 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-0.41 Å20.55 Å2
2--0.39 Å20.56 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16111 0 261 1328 17700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02216850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9822880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53752003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.99223.571784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.338152800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.91315112
X-RAY DIFFRACTIONr_chiral_restr0.1520.22434
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112795
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1631.510047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.003216205
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.40536803
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2224.56675
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A556medium positional0.140.5
2B556medium positional0.150.5
3C556medium positional0.150.5
4D556medium positional0.20.5
5E556medium positional0.170.5
6F556medium positional0.150.5
7G556medium positional0.180.5
8H556medium positional0.190.5
1A580loose positional0.355
2B580loose positional0.315
3C580loose positional0.425
4D580loose positional0.425
5E580loose positional0.445
6F580loose positional0.355
7G580loose positional0.385
8H580loose positional0.45
1A556medium thermal2.732
2B556medium thermal1.352
3C556medium thermal2.492
4D556medium thermal1.272
5E556medium thermal1.192
6F556medium thermal1.422
7G556medium thermal2.872
8H556medium thermal2.62
1A580loose thermal2.6210
2B580loose thermal1.7210
3C580loose thermal2.4310
4D580loose thermal1.8910
5E580loose thermal1.5810
6F580loose thermal1.7610
7G580loose thermal2.4610
8H580loose thermal2.2910
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 580 -
Rwork0.229 10860 -
obs--92.58 %
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)
10.93420.1001-0.35490.4848-0.06911.5792-0.01110.1305-0.04610.020.02380.00940.0781-0.0524-0.01270.01240.009-0.01950.0681-0.01050.1306-0.23071.26140.5376
20.34160.1360.1811.0634-0.7651.66060.00080.0005-0.05680.11780.117-0.0021-0.095-0.1217-0.11780.03530.015-0.01260.08420.0010.0992-15.7553-30.937267.4886
30.94860.02360.46191.0094-0.01760.904-0.0208-0.13820.0149-0.03490.03970.0257-0.034-0.0807-0.01890.0043-0.0099-0.0010.1040.00020.1157-28.8139-25.40839.3969
41.1643-0.1868-0.19460.5303-0.1340.6384-0.0065-0.1829-0.02920.16930.08390.0663-0.0406-0.025-0.07740.08640.04110.00440.0913-0.01050.0988-14.21929.672226.5131
50.4434-0.1175-0.17650.9566-0.74881.6952-0.02380.00340.0649-0.08170.0584-0.05750.0796-0.0277-0.03460.04690.02580.00750.0694-0.00620.093113.02257.742-27.3008
61.3540.2568-0.15010.5625-0.06811.0246-0.09350.13590.0964-0.33910.15950.13420.0477-0.0405-0.0660.2261-0.0774-0.07220.06490.02850.1228-42.5837-34.25713.4364
70.69870.20680.05490.9576-0.99961.5586-0.1301-0.2124-0.03320.37230.19260.0734-0.6557-0.2571-0.06250.34720.12090.0130.16520.01480.0593-13.3211-27.469198.2102
80.7896-0.2895-0.23111.022-0.76731.5236-0.1360.29450.0366-0.2560.12460.01740.6037-0.23690.01140.2894-0.06490.01380.20660.02050.054615.24744.8751-57.9812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 301
2X-RAY DIFFRACTION2B1 - 301
3X-RAY DIFFRACTION3C0 - 301
4X-RAY DIFFRACTION4D1 - 301
5X-RAY DIFFRACTION5E1 - 301
6X-RAY DIFFRACTION6F1 - 5573
7X-RAY DIFFRACTION7G0 - 301
8X-RAY DIFFRACTION8H1 - 301

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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