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- PDB-6qky: Tryptophan synthase subunit alpha from Streptococcus pneumoniae w... -

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Basic information

Entry
Database: PDB / ID: 6qky
TitleTryptophan synthase subunit alpha from Streptococcus pneumoniae with 3D domain swap in the core of TIM barrel
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / tryptophan synthase / TIM barrel / 3D domain swapping / protein oligomerization / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.54 Å
AuthorsMichalska, K. / Kowiel, M. / Bigelow, L. / Endres, M. / Gilski, M. / Jaskolski, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: 3D domain swapping in the TIM barrel of the alpha subunit of Streptococcus pneumoniae tryptophan synthase.
Authors: Michalska, K. / Kowiel, M. / Bigelow, L. / Endres, M. / Gilski, M. / Jaskolski, M. / Joachimiak, A.
History
DepositionJan 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Tryptophan synthase alpha chain
B: Tryptophan synthase alpha chain
C: Tryptophan synthase alpha chain
D: Tryptophan synthase alpha chain
E: Tryptophan synthase alpha chain
F: Tryptophan synthase alpha chain
G: Tryptophan synthase alpha chain
H: Tryptophan synthase alpha chain
I: Tryptophan synthase alpha chain
J: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,87525
Polymers281,78610
Non-polymers1,08915
Water6,107339
1
A: Tryptophan synthase alpha chain
B: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6766
Polymers56,3572
Non-polymers3184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-82 kcal/mol
Surface area23260 Å2
MethodPISA
2
C: Tryptophan synthase alpha chain
D: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6626
Polymers56,3572
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-88 kcal/mol
Surface area23060 Å2
MethodPISA
3
E: Tryptophan synthase alpha chain
F: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5835
Polymers56,3572
Non-polymers2263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-83 kcal/mol
Surface area22040 Å2
MethodPISA
4
G: Tryptophan synthase alpha chain
H: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4774
Polymers56,3572
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-87 kcal/mol
Surface area22200 Å2
MethodPISA
5
I: Tryptophan synthase alpha chain
J: Tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4774
Polymers56,3572
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-85 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.810, 138.620, 107.250
Angle α, β, γ (deg.)90.00, 117.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLNGLNAA0 - 2573 - 260
21ALAALAGLNGLNBB0 - 2573 - 260
12MSEMSELYSLYSAA1 - 2584 - 261
22MSEMSELYSLYSCC1 - 2584 - 261
13MSEMSELYSLYSAA1 - 2584 - 261
23MSEMSELYSLYSDD1 - 2584 - 261
14MSEMSEGLNGLNAA1 - 2574 - 260
24MSEMSEGLNGLNEE1 - 2574 - 260
15MSEMSELYSLYSAA1 - 2584 - 261
25MSEMSELYSLYSFF1 - 2584 - 261
16ALAALALYSLYSAA0 - 2583 - 261
26ALAALALYSLYSGG0 - 2583 - 261
17MSEMSELYSLYSAA1 - 2584 - 261
27MSEMSELYSLYSHH1 - 2584 - 261
18MSEMSEGLNGLNAA1 - 2574 - 260
28MSEMSEGLNGLNII1 - 2574 - 260
19MSEMSELYSLYSAA1 - 2584 - 261
29MSEMSELYSLYSJJ1 - 2584 - 261
110MSEMSELYSLYSBB1 - 2584 - 261
210MSEMSELYSLYSCC1 - 2584 - 261
111MSEMSELYSLYSBB1 - 2584 - 261
211MSEMSELYSLYSDD1 - 2584 - 261
112MSEMSETYRTYRBB1 - 2564 - 259
212MSEMSETYRTYREE1 - 2564 - 259
113MSEMSELYSLYSBB1 - 2584 - 261
213MSEMSELYSLYSFF1 - 2584 - 261
114ALAALALYSLYSBB0 - 2583 - 261
214ALAALALYSLYSGG0 - 2583 - 261
115MSEMSEGLNGLNBB1 - 2574 - 260
215MSEMSEGLNGLNHH1 - 2574 - 260
116MSEMSEGLNGLNBB1 - 2574 - 260
216MSEMSEGLNGLNII1 - 2574 - 260
117MSEMSELYSLYSBB1 - 2584 - 261
217MSEMSELYSLYSJJ1 - 2584 - 261
118MSEMSELYSLYSCC1 - 2584 - 261
218MSEMSELYSLYSDD1 - 2584 - 261
119MSEMSEGLNGLNCC1 - 2574 - 260
219MSEMSEGLNGLNEE1 - 2574 - 260
120MSEMSELYSLYSCC1 - 2584 - 261
220MSEMSELYSLYSFF1 - 2584 - 261
121MSEMSELYSLYSCC1 - 2584 - 261
221MSEMSELYSLYSGG1 - 2584 - 261
122MSEMSELYSLYSCC1 - 2584 - 261
222MSEMSELYSLYSHH1 - 2584 - 261
123MSEMSELYSLYSCC1 - 2584 - 261
223MSEMSELYSLYSII1 - 2584 - 261
124MSEMSELYSLYSCC1 - 2584 - 261
224MSEMSELYSLYSJJ1 - 2584 - 261
125MSEMSEGLNGLNDD1 - 2574 - 260
225MSEMSEGLNGLNEE1 - 2574 - 260
126MSEMSELYSLYSDD1 - 2584 - 261
226MSEMSELYSLYSFF1 - 2584 - 261
127MSEMSELYSLYSDD1 - 2584 - 261
227MSEMSELYSLYSGG1 - 2584 - 261
128MSEMSELYSLYSDD1 - 2584 - 261
228MSEMSELYSLYSHH1 - 2584 - 261
129MSEMSELYSLYSDD1 - 2584 - 261
229MSEMSELYSLYSII1 - 2584 - 261
130MSEMSELYSLYSDD1 - 2584 - 261
230MSEMSELYSLYSJJ1 - 2584 - 261
131MSEMSEGLNGLNEE1 - 2574 - 260
231MSEMSEGLNGLNFF1 - 2574 - 260
132MSEMSEGLNGLNEE1 - 2574 - 260
232MSEMSEGLNGLNGG1 - 2574 - 260
133MSEMSEGLNGLNEE1 - 2574 - 260
233MSEMSEGLNGLNHH1 - 2574 - 260
134MSEMSEGLNGLNEE1 - 2574 - 260
234MSEMSEGLNGLNII1 - 2574 - 260
135MSEMSEGLNGLNEE1 - 2574 - 260
235MSEMSEGLNGLNJJ1 - 2574 - 260
136MSEMSELYSLYSFF1 - 2584 - 261
236MSEMSELYSLYSGG1 - 2584 - 261
137MSEMSELYSLYSFF1 - 2584 - 261
237MSEMSELYSLYSHH1 - 2584 - 261
138MSEMSELYSLYSFF1 - 2584 - 261
238MSEMSELYSLYSII1 - 2584 - 261
139MSEMSELYSLYSFF1 - 2584 - 261
239MSEMSELYSLYSJJ1 - 2584 - 261
140MSEMSELYSLYSGG1 - 2584 - 261
240MSEMSELYSLYSHH1 - 2584 - 261
141MSEMSELYSLYSGG1 - 2584 - 261
241MSEMSELYSLYSII1 - 2584 - 261
142MSEMSELYSLYSGG1 - 2584 - 261
242MSEMSELYSLYSJJ1 - 2584 - 261
143MSEMSELYSLYSHH1 - 2584 - 261
243MSEMSELYSLYSII1 - 2584 - 261
144MSEMSELYSLYSHH1 - 2584 - 261
244MSEMSELYSLYSJJ1 - 2584 - 261
145MSEMSELYSLYSII1 - 2584 - 261
245MSEMSELYSLYSJJ1 - 2584 - 261

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#1: Protein
Tryptophan synthase alpha chain


Mass: 28178.627 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: SEMET DERIVATIVE / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: trpA, SP_1811 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q97P33, tryptophan synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M Na acetate, 0.085 M Tris/HCl, pH 8.5, 25% PEG 4K, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.54→48.99 Å / Num. obs: 171460 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 1.93 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.53
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 24979 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.54→48.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 29.919 / SU ML: 0.294 / Cross valid method: FREE R-VALUE / ESU R: 0.683 / ESU R Free: 0.282 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITION
RfactorNum. reflection% reflectionSelection details
Rfree0.23435 2091 1.2 %RANDOM
Rwork0.19304 ---
obs0.19353 171460 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-1.1 Å2
2--1.13 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.54→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18886 0 72 339 19297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01519418
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718193
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.75126449
X-RAY DIFFRACTIONr_angle_other_deg0.4061.72642300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50452531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08421.548504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91152496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2571542
X-RAY DIFFRACTIONr_chiral_restr0.0540.22695
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02121816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023429
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_it1.5433.91910128
X-RAY DIFFRACTIONr_mcbond_other1.5243.91510119
X-RAY DIFFRACTIONr_mcangle_it2.5195.86612630
X-RAY DIFFRACTIONr_mcangle_other2.5195.86712631
X-RAY DIFFRACTIONr_scbond_it1.6884.129290
X-RAY DIFFRACTIONr_scbond_other1.6874.129291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7726.10613813
X-RAY DIFFRACTIONr_long_range_B_refined4.49449.54220112
X-RAY DIFFRACTIONr_long_range_B_other4.49549.54520113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A68490.12
12B68490.12
21A71340.07
22C71340.07
31A70800.08
32D70800.08
41A68080.11
42E68080.11
51A68740.09
52F68740.09
61A67910.1
62G67910.1
71A70610.08
72H70610.08
81A68850.11
82I68850.11
91A68890.11
92J68890.11
101B68590.12
102C68590.12
111B68130.11
112D68130.11
121B68280.1
122E68280.1
131B67510.1
132F67510.1
141B67040.11
142G67040.11
151B67410.12
152H67410.12
161B68850.1
162I68850.1
171B68970.1
172J68970.1
181C70440.08
182D70440.08
191C67710.11
192E67710.11
201C68490.09
202F68490.09
211C67480.09
212G67480.09
221C70050.09
222H70050.09
231C68920.11
232I68920.11
241C69200.11
242J69200.11
251D67780.11
252E67780.11
261D67880.09
262F67880.09
271D67080.1
272G67080.1
281D69300.09
282H69300.09
291D68470.11
292I68470.11
301D68610.11
302J68610.11
311E67280.1
312F67280.1
321E66630.1
322G66630.1
331E67630.11
332H67630.11
341E69950.08
342I69950.08
351E70140.08
352J70140.08
361F67900.1
362G67900.1
371F67520.1
372H67520.1
381F68220.1
382I68220.1
391F67750.1
392J67750.1
401G66410.11
402H66410.11
411G67200.11
412I67200.11
421G67030.11
422J67030.11
431H68650.11
432I68650.11
441H68370.11
442J68370.11
451I70850.09
452J70850.09
LS refinement shellResolution: 2.545→2.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 79 -
Rwork0.348 6496 -
obs--99.91 %
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)
16.3646-0.11-1.06795.19791.03163.4269-0.18750.139-0.5282-0.0350.01570.33330.143-0.41370.17180.1649-0.05850.01940.235-0.03370.1527-31.66269.78922.435
219.97879.069615.29877.46637.524611.88150.43690.9976-0.6909-0.3252-0.08830.32180.17030.7365-0.34860.33590.0668-0.03020.2733-0.01480.3672.07380.55623.196
35.71980.6299-1.82869.6447-2.99867.85710.1345-0.18990.16910.1639-0.06750.1699-0.4584-0.2305-0.0670.1971-0.04840.0060.1673-0.0370.0141-1.55296.08225.954
47.41851.086-1.33463.5623-0.68622.5302-0.03570.51840.1646-0.3424-0.03960.2145-0.2963-0.22690.07530.29120.0091-0.00160.2037-0.01070.0298-4.60493.84311.011
52.8709-0.0462-1.096111.22922.913410.4596-0.23090.3641-0.6388-0.51540.20090.28840.2565-0.65580.02990.2482-0.07970.09060.2094-0.04590.18014.61182.2011.444
61.53223.4655-2.823518.7014-2.29856.7444-0.23110.1933-0.00740.27740.3153-0.27360.7241-0.3632-0.08430.5618-0.0290.02750.53750.08420.500312.40169.5577.07
79.0542-4.37392.95395.75330.2842.55190.19030.397-0.1186-0.0812-0.1848-0.730.52510.3854-0.00550.4289-0.00260.26920.26760.08420.388416.04183.9237.245
813.9064.0074-10.04736.1136-2.017614.43310.0058-1.1884-0.41150.0611-0.3114-0.9829-0.05421.58120.30570.2538-0.00390.00220.31880.07360.326118.23489.8822.767
92.57590.3571-0.78813.71721.19483.88510.1041-0.07710.2185-0.29180.0048-0.2053-0.5160.2242-0.1090.2338-0.03180.07090.06740.01040.10868.6796.98315.888
1026.986327.7282-22.807228.585-23.471219.32171.4176-1.37870.15251.2452-1.32670.2301-1.03261.1902-0.09090.7331-0.0986-0.00570.6302-0.14920.457-15.60881.25230.133
115.6226-0.2188-0.88053.9833-0.24342.6916-0.03910.3522-0.0334-0.31060.0154-0.19930.0109-0.3510.02380.1765-0.02120.02180.2387-0.04120.072-23.35576.30416.843
123.626-0.0950.118612.32020.20672.5997-0.06210.0590.8628-0.1873-0.1128-0.0396-0.5965-0.26430.17480.38590.11430.03690.3788-0.00060.3074-33.71691.09222.006
131.38082.89510.840711.38111.85760.53010.3074-0.5861-0.0224-1.4615-0.3980.37650.1511-0.36540.09061.2720.0377-0.03711.1085-0.09110.9008-35.293.78442.205
142.1489-1.6965-3.233113.649-1.84846.70060.2191-0.03520.10261.59890.00680.5859-1.1929-0.2569-0.22590.47950.2192-0.05930.7219-0.12420.3973-38.61487.3128.69
1518.883-11.412712.80814.1774-9.68389.2078-0.41670.10390.46040.47740.33230.5399-0.3296-0.05410.08440.5563-0.03620.13790.87050.01210.2654-38.8378.04438.756
169.6642-3.07970.04358.1525-2.95084.7548-0.2623-0.7015-0.68580.66480.16250.41530.0705-0.07470.09990.2887-0.00850.07360.4327-0.0120.123-34.6270.11334.771
173.90020.4574-1.13512.6132-0.23017.70310.1857-0.04690.0644-0.01-0.09990.26740.8368-0.4777-0.08570.3868-0.06280.05190.2442-0.0170.1139-38.85271.35561.784
184.01660.4593-1.28523.9167-0.34283.4815-0.0321-0.3826-0.02180.3520.1121-0.01240.06450.1277-0.080.3910.0722-0.06270.20480.04230.056-13.99499.8657.666
1911.43821.06391.1987.73890.33997.65920.1844-0.50840.47570.0891-0.21520.5343-0.518-0.78120.03070.36150.10220.06790.17390.01260.0748-23.272105.2753.906
203.2382-0.22862.59020.6512-1.448510.0697-0.1413-0.30120.17970.12880.09940.44570.1611-0.78890.0420.40390.08790.07370.1831-0.03850.4808-26.798108.16645.879
2110.53126.50453.653311.71897.17374.40860.8982-1.61950.99751.9708-0.4305-0.68821.2175-0.2175-0.46771.05490.0175-0.08540.9328-0.06860.9225-21.73991.47427.354
225.86653.1964.0076.74624.091713.2503-0.02680.585-0.3564-0.7020.01560.4518-0.2690.14530.01120.46570.0961-0.0050.17610.02080.2007-21.764108.23432.846
234.4078-1.02230.57762.2086-0.71354.20640.20460.0944-0.2094-0.31550.0053-0.02480.06740.5479-0.20980.30760.01350.00520.1857-0.05220.1607-7.386102.96437.589
2411.5499-6.60082.279524.1769-6.24835.79220.31510.42130.3805-1.2285-0.2804-0.55950.13070.8573-0.03470.385-0.07920.00230.3777-0.07380.17040.078108.7538.39
256.70754.1352-1.27318.6354-6.765711.47930.7178-0.44381.27760.8709-0.22190.7405-1.29220.6089-0.49590.77590.0009-0.00860.12-0.15190.3362-14.949119.4845.914
263.35590.8288-0.82424.799-2.52515.7592-0.0758-0.3903-0.26460.4137-0.0293-0.2556-0.19260.52550.10520.36520.067-0.05180.2455-0.01760.0422-6.195103.05952.342
272.25861.3443-0.75314.69520.38785.9526-0.00510.30560.26440.1657-0.01070.16690.04370.15820.01580.31690.0220.08540.3120.01790.0872-34.02380.03954.635
2812.94976.63451.282413.53343.2247.2993-0.0598-0.36311.08810.1957-0.10740.76-0.8749-0.02780.16710.39660.0390.13970.26880.0280.1783-35.95687.7764.083
294.540.95832.20743.2126-0.331211.74860.0648-0.54570.40380.3309-0.3544-0.027-0.5761-0.04570.28960.3353-0.08780.18560.2944-0.09340.2-35.07185.23773.837
301.38250.79756.76940.56314.048334.5282-0.50830.30080.2762-0.2643-0.16150.2209-1.58811.3740.66981.41380.2176-0.04511.2461-0.22771.0837-14.16177.1883.027
316.1164-0.72242.26195.7384-1.36768.75010.2456-0.8909-0.07030.3005-0.0674-0.51541.00360.3444-0.17830.5542-0.13940.13090.4229-0.02350.1744-31.81872.17179.666
328.0605-0.699-1.81783.32784.07798.93030.1822-0.1713-0.70490.601-0.2297-0.49441.4101-0.00280.04760.88660.0531-0.00550.17920.04090.2692-32.27261.88265.541
335.6693-1.95371.70079.5765-2.84647.4367-0.1817-0.4607-0.29610.64670.19130.86190.4138-0.1789-0.00950.4011-0.06080.02360.06680.09080.4098-10.03944.15779.089
341.8645-0.09410.083115.9522.00471.9805-0.1895-0.01060.03570.20210.19760.7186-0.0451-0.076-0.00820.263-0.0256-0.05510.26220.15970.241-9.41852.39874.455
356.4716-2.37342.00476.57472.54155.90830.123-0.1131-0.18990.36240.0899-0.40050.0433-0.0079-0.21280.3469-0.1212-0.09760.29540.06080.288811.67380.13679.282
363.5766-0.41440.31124.1177-1.27442.6526-0.0869-0.7351-0.34310.8958-0.01140.096-0.0019-0.03310.09820.6793-0.0464-0.07660.3770.00340.141-2.15879.69690.308
3714.2844-4.15791.7915.2907-1.71632.0014-0.0283-0.1822-0.23180.31480.02620.4361-0.1108-0.80230.0020.6395-0.06880.01820.4556-0.02170.3651-13.63491.20584.053
381.4607-1.7814-3.70694.17692.485615.60420.09350.2420.302-0.5628-0.046-0.2534-0.13970.6351-0.04750.6655-0.005-0.16980.75290.16370.6238-5.83596.80675.483
398.3169-5.5237-6.039211.77076.88225.9041-0.3920.99360.20890.3228-0.20540.48750.3372-0.4210.59740.4998-0.0556-0.07550.39590.1790.6185-3.31795.13277.237
406.54011.3482-1.52438.38051.26877.27270.66170.32411.2474-0.3413-0.3566-0.4487-1.30350.0672-0.30521.35410.34490.7320.65110.67861.29497.07696.44671.478
4114.6473-10.77387.652217.9005-0.27526.8874-0.7762-1.2139-0.25731.86180.51611.0370.3256-0.79220.261.0144-0.1602-0.10790.7291-0.15890.30491.58591.56697.489
425.2903-2.5347-0.52725.06111.61163.5046-0.04250.09140.76450.38360.0467-0.6329-0.21060.2706-0.00410.5012-0.1224-0.1990.2637-0.00830.28628.37990.45881.369
4311.7615-4.3002-2.46995.6565.84016.7106-0.2071-1.37220.4073-0.60011.8876-1.5826-0.88461.8615-1.68050.6876-0.2424-0.15520.675-0.42470.99781.65858.46970.813
442.3070.2207-0.39517.07411.64983.9078-0.1901-0.5768-0.01961.16140.25710.6480.2190.0273-0.0670.57370.01050.01880.27490.09690.3358-8.6255.84684.258
458.34454.17297.35535.0908-2.684220.91340.6698-0.3814-0.54420.6487-0.2359-0.48940.12250.644-0.43380.880.2762-0.2920.8579-0.31570.77114.47246.07491.82
467.11251.3621-10.44292.6744-6.707927.7234-0.2426-0.59130.1988-0.10240.3585-0.54580.31571.0448-0.11590.82950.0981-0.12870.8337-0.10310.987312.23342.08384.927
472.19510.7435-1.88093.9388-1.788611.536-0.3105-0.224-0.15340.62620.2826-0.53370.40250.96160.02790.56840.085-0.14680.31970.08160.42224.40139.39478.553
484.0873-1.12183.3046.5152-2.357211.262-0.12610.1733-0.46460.10380.026-0.02170.40130.30390.10010.2947-0.1113-0.04780.21310.04610.3787-2.20140.07269.66
4912.6133-0.01393.68435.98677.13918.140.1885-0.536-1.07670.0365-0.1115-0.571.3662-0.3274-0.07711.30060.13370.05960.1669-0.03140.854521.32419.02745.872
502.7357-0.4066-0.7493.26553.59988.6749-0.1073-0.0451-0.4737-0.03450.0206-0.22591.0967-0.05020.08670.78980.0068-0.12640.03670.07610.42948.22532.17750.348
510.76071.11521.38497.21132.4122.5715-0.11130.10940.22110.0258-0.29180.4589-0.12830.24980.40310.2664-0.0048-0.09030.71310.03410.467625.42760.26258.31
526.223.54230.37936.70992.53853.673-0.03790.1353-0.0167-0.06610.1201-0.62960.20860.6795-0.08220.32940.0699-0.11470.75910.0560.432638.32356.93862.34
534.08170.87620.47327.26310.46533.9346-0.0776-0.2229-0.27460.59520.0949-0.23630.91530.4892-0.01740.49190.1136-0.19010.71290.0350.539435.72551.0871.933
5416.4685-4.7785.045317.2608-9.85546.04170.355-0.4618-0.9320.0158-0.31460.09090.21650.0607-0.04051.0056-0.09540.13030.7292-0.12780.577333.58153.44780.747
550.68760.7818-0.60161.0468-0.73110.550.26610.1664-0.02270.568-0.11480.278-0.2628-0.1019-0.15131.4716-0.05210.0491.4484-0.23981.245727.09757.72688.791
562.9904-1.9825-0.72974.3964-2.00914.2003-0.0723-0.45820.31080.64790.1277-0.044-0.19690.2281-0.05540.551-0.1569-0.16810.6713-0.0960.54427.82971.91277.191
574.5621-0.6376-2.570418.069711.044517.36740.0795-0.4684-0.04470.40210.3188-1.02040.08430.6775-0.39820.4407-0.0283-0.23020.8517-0.05440.533643.77362.94880.352
580.97781.59171.90373.12084.02578.65490.02520.01880.07170.02110.1313-0.0588-0.20670.6198-0.15650.2455-0.0485-0.10320.64-0.01750.514732.71367.21763.222
594.5379-0.0080.46664.21130.28793.99090.0526-0.3628-0.29620.0182-0.0295-0.42360.81620.6921-0.0230.5240.1395-0.13250.22130.08770.368518.26236.14757.671
6046.56456.415218.610522.3664-13.15919.0792-0.33380.2328-0.3336-1.23950.2256-0.05380.65590.14930.10820.76310.3254-0.06160.78540.1430.69132.16532.15559.489
617.54757.7754-3.22518.1436-4.7611.6010.5048-0.1842-0.4458-0.5419-0.47221.00980.07610.2156-0.03261.33590.8196-0.10930.60060.1130.792427.33730.30549.74
6214.01160.2635-2.1988.205-0.39892.5443-0.2967-0.2646-0.0462-0.29160.0601-0.7320.04360.98110.23660.82020.24320.01150.5189-0.04410.547531.42433.4140.77
632.1151-0.1448-2.73423.0126-1.51854.8548-0.2510.1828-0.1782-0.2801-0.1643-0.27120.77360.35480.41541.17810.3044-0.00650.7709-0.04640.566922.95333.17933.285
645.3028-1.6884-3.072119.528215.719213.4836-0.17230.4569-0.4241-1.0326-0.4480.4148-0.3119-0.5410.62031.0912-0.0941-0.06830.26140.09580.53755.68434.4839.626
6511.6434-6.14524.37811.86743.38665.44630.19521.6645-0.2863-0.11140.3138-0.56960.06381.3806-0.50890.8226-0.10580.12740.4513-0.2190.29973.51941.8151.527
664.0986-0.56711.80872.6064-1.20188.45680.257-0.1278-0.02620.0161-0.15890.14590.5984-0.3047-0.09820.4324-0.09180.0250.1035-0.07730.2339-1.51744.54717.603
6711.11969.46560.791132.16972.26290.17750.2323-0.1866-0.40150.9892-0.28030.96940.1863-0.03060.04810.8918-0.1412-0.10340.54710.01030.477421.66163.64434.486
682.92030.38940.47623.2455-1.22694.56390.04910.4082-0.0213-0.3981-0.2885-0.41510.13740.9560.23930.21620.02540.13350.50390.03260.288929.49868.12619.847
693.5942-0.5587-0.03114.1517-1.95567.45940.11390.3963-0.736-0.6408-0.1073-0.39040.93840.8723-0.00650.38480.21910.24720.67820.00050.5835.51955.13719.708
703.56891.51640.874714.06262.59520.59820.42180.9334-0.6109-0.3846-0.3475-0.13770.10580.1268-0.07430.71340.31980.16240.91810.07680.710740.35449.38927.879
710.3449-0.64161.11024.3883-3.36124.53780.24350.0351-0.18160.5766-0.2434-0.24760.62360.8164-0.00010.70610.2063-0.01141.26140.2680.738540.26454.86539.836
728.2758-5.37761.87477.90640.83056.5533-0.4569-0.58280.26670.3725-0.0183-0.6276-0.33710.72850.47530.3003-0.11140.03160.60650.14760.390836.04572.3740.747
7313.44045.00866.96539.2977-1.91486.56580.08940.9254-0.4612-0.65570.59670.1190.20390.5172-0.68610.45460.01510.3691.07280.05280.760948.91864.64325.623
747.1174-1.41372.57272.0149-1.77535.7782-0.11130.2377-0.09880.1121-0.2419-0.2769-0.27930.65230.35310.1452-0.08470.08020.47010.01450.337432.75973.7729.764
7520.741512.5721-11.50819.2994-3.382314.13080.39580.10951.14350.3471-0.00320.71360.0083-0.2079-0.39250.53270.1138-0.0810.28610.03280.78524.17358.83624.272
763.26870.31842.53952.40581.19815.7240.22250.1204-0.2564-0.0679-0.1109-0.54690.74680.3557-0.11160.57020.03810.03490.1456-0.03850.316110.77743.78719.654
778.06842.4192-0.92182.8948-1.75226.29760.03850.8613-0.4016-0.3967-0.1104-0.84380.31440.69090.07190.41270.0660.0950.39-0.040.336514.34849.2638.492
782.4903-0.46751.562312.8956-0.99733.29150.03570.38690.3016-0.5342-0.0368-0.07490.0330.49220.00110.3748-0.01730.08890.3241-0.04580.25295.96957.7533.763
790.76040.2659-0.6663.4517-1.11811.71320.12360.25710.4235-0.2737-0.06370.6232-0.5544-0.3097-0.05990.674-0.0273-0.07430.4043-0.05740.6035-5.84760.9566.534
808.30781.17226.38917.44560.074712.67690.1825-0.63550.4111-0.1759-0.31720.75180.529-1.89530.13460.3555-0.09310.13560.523-0.00430.4016-11.90249.57720.134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 59
2X-RAY DIFFRACTION2A60 - 67
3X-RAY DIFFRACTION3A68 - 93
4X-RAY DIFFRACTION4A94 - 152
5X-RAY DIFFRACTION5A153 - 177
6X-RAY DIFFRACTION6A178 - 196
7X-RAY DIFFRACTION7A197 - 231
8X-RAY DIFFRACTION8A232 - 258
9X-RAY DIFFRACTION9B-2 - 57
10X-RAY DIFFRACTION10B58 - 65
11X-RAY DIFFRACTION11B66 - 158
12X-RAY DIFFRACTION12B159 - 178
13X-RAY DIFFRACTION13B186 - 192
14X-RAY DIFFRACTION14B193 - 214
15X-RAY DIFFRACTION15B215 - 224
16X-RAY DIFFRACTION16B225 - 258
17X-RAY DIFFRACTION17C1 - 59
18X-RAY DIFFRACTION18C60 - 118
19X-RAY DIFFRACTION19C119 - 137
20X-RAY DIFFRACTION20C138 - 178
21X-RAY DIFFRACTION21C179 - 189
22X-RAY DIFFRACTION22C190 - 212
23X-RAY DIFFRACTION23C213 - 243
24X-RAY DIFFRACTION24C244 - 258
25X-RAY DIFFRACTION25D1 - 17
26X-RAY DIFFRACTION26D18 - 60
27X-RAY DIFFRACTION27D61 - 119
28X-RAY DIFFRACTION28D120 - 140
29X-RAY DIFFRACTION29D141 - 179
30X-RAY DIFFRACTION30D180 - 190
31X-RAY DIFFRACTION31D191 - 228
32X-RAY DIFFRACTION32D229 - 258
33X-RAY DIFFRACTION33E1 - 39
34X-RAY DIFFRACTION34E40 - 63
35X-RAY DIFFRACTION35E64 - 95
36X-RAY DIFFRACTION36E96 - 168
37X-RAY DIFFRACTION37E169 - 206
38X-RAY DIFFRACTION38E207 - 224
39X-RAY DIFFRACTION39E225 - 235
40X-RAY DIFFRACTION40E236 - 257
41X-RAY DIFFRACTION41F1 - 7
42X-RAY DIFFRACTION42F8 - 58
43X-RAY DIFFRACTION43F59 - 69
44X-RAY DIFFRACTION44F70 - 159
45X-RAY DIFFRACTION45F160 - 176
46X-RAY DIFFRACTION46F177 - 202
47X-RAY DIFFRACTION47F203 - 222
48X-RAY DIFFRACTION48F223 - 258
49X-RAY DIFFRACTION49G1 - 16
50X-RAY DIFFRACTION50G17 - 55
51X-RAY DIFFRACTION51G56 - 87
52X-RAY DIFFRACTION52G88 - 116
53X-RAY DIFFRACTION53G117 - 162
54X-RAY DIFFRACTION54G163 - 177
55X-RAY DIFFRACTION55G178 - 205
56X-RAY DIFFRACTION56G206 - 258
57X-RAY DIFFRACTION57H1 - 17
58X-RAY DIFFRACTION58H18 - 63
59X-RAY DIFFRACTION59H64 - 136
60X-RAY DIFFRACTION60H137 - 143
61X-RAY DIFFRACTION61H144 - 156
62X-RAY DIFFRACTION62H157 - 180
63X-RAY DIFFRACTION63H186 - 232
64X-RAY DIFFRACTION64H233 - 258
65X-RAY DIFFRACTION65I1 - 8
66X-RAY DIFFRACTION66I9 - 59
67X-RAY DIFFRACTION67I60 - 69
68X-RAY DIFFRACTION68I70 - 132
69X-RAY DIFFRACTION69I133 - 157
70X-RAY DIFFRACTION70I158 - 176
71X-RAY DIFFRACTION71I177 - 228
72X-RAY DIFFRACTION72I229 - 258
73X-RAY DIFFRACTION73J1 - 15
74X-RAY DIFFRACTION74J16 - 59
75X-RAY DIFFRACTION75J60 - 68
76X-RAY DIFFRACTION76J69 - 119
77X-RAY DIFFRACTION77J120 - 145
78X-RAY DIFFRACTION78J146 - 180
79X-RAY DIFFRACTION79J184 - 232
80X-RAY DIFFRACTION80J233 - 258

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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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