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- PDB-2x2y: Cellulomonas fimi endo-beta-1,4-mannanase double mutant -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2x2y
TitleCellulomonas fimi endo-beta-1,4-mannanase double mutant
ComponentsMAN26A
KeywordsHYDROLASE / CLAN GH-A / FAMILY 26 / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Bacterial Ig domain / Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. ...Bacterial Ig domain / Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Galactose-binding-like domain superfamily / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Man26A
Similarity search - Component
Biological speciesCELLULOMONAS FIMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHekmat, O. / Lo Leggio, L. / Rosengren, A. / Kamarauskaite, J. / Kolenova, K. / Staalbrand, H.
CitationJournal: Biochemistry / Year: 2010
Title: Rational Engineering of Mannosyl Binding in the Distal Glycone Subsites of Cellulomonas Fimi Endo-Beta-1,4-Mannanase: Mannosyl Binding Promoted at Subsite -2 and Demoted at Subsite -3 .
Authors: Hekmat, O. / Lo Leggio, L. / Rosengren, A. / Kamarauskaite, J. / Kolenova, K. / Stalbrand, H.
History
DepositionJan 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAN26A
B: MAN26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,39814
Polymers100,9322
Non-polymers46512
Water11,259625
1
A: MAN26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6075
Polymers50,4661
Non-polymers1414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MAN26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7919
Polymers50,4661
Non-polymers3258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.093, 99.555, 132.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111A
211B
112A
212B
113A
213B
114A
214B
115A
215B
116A
216B
117A
217B
118A
218B
119A
219B
120A
220B
121A
221B
122A
222B
123A
223B
124A
224B
125A
225B
126A
226B
127A
227B
128A
228B
129A
229B
130A
230B
131A
231B
3232

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLY1AA447 - 456447 - 456
21VALVALGLYGLY1BB447 - 456447 - 456
12GLUGLUGLUGLU1AA44
22GLUGLUGLUGLU1BB44
13HISHISLEULEU1AA141 - 231141 - 231
23HISHISLEULEU1BB141 - 231141 - 231
14GLUGLUGLUGLU3AA3030
24GLUGLUGLUGLU3BB3030
15ARGARGARGARG3AA7979
25ARGARGARGARG3BB7979
16ARGARGARGARG3AA232232
26ARGARGARGARG3BB232232
17LEULEULEULEU3AA245245
27LEULEULEULEU3BB245245
18GLNGLNGLNGLN1AA329329
28GLNGLNGLNGLN1BB329329
19GLUGLUGLUGLU3AA341341
29GLUGLUGLUGLU3BB341341
110GLNGLNGLNGLN3AA372372
210GLNGLNGLNGLN3BB372372
111THRTHRTHRTHR3AA391391
211THRTHRTHRTHR3BB391391
112GLNGLNGLNGLN3AA403403
212GLNGLNGLNGLN3BB403403
113ASPASPASPASP3AA420420
213ASPASPASPASP3BB420420
114THRTHRTHRTHR3AA446446
214THRTHRTHRTHR3BB446446
115THRTHRALAALA1AA5 - 115 - 11
215THRTHRALAALA1BB5 - 115 - 11
116ALAALAGLYGLY1AA13 - 2913 - 29
216ALAALAGLYGLY1BB13 - 2913 - 29
117GLYGLYGLUGLU1AA31 - 7831 - 78
217GLYGLYGLUGLU1BB31 - 7831 - 78
118PROPROALAALA1AA80 - 8380 - 83
218PROPROALAALA1BB80 - 8380 - 83
119THRTHRGLYGLY1AA233 - 244233 - 244
219THRTHRGLYGLY1BB233 - 244233 - 244
120ASPASPGLYGLY1AA246 - 328246 - 328
220ASPASPGLYGLY1BB246 - 328246 - 328
121HISHISLEULEU1AA330 - 340330 - 340
221HISHISLEULEU1BB330 - 340330 - 340
122ASPASPALAALA1AA342 - 371342 - 371
222ASPASPALAALA1BB342 - 371342 - 371
123PROPROPROPRO1AA373 - 390373 - 390
223PROPROPROPRO1BB373 - 390373 - 390
124THRTHRVALVAL1AA392 - 402392 - 402
224THRTHRVALVAL1BB392 - 402392 - 402
125SERSERLEULEU1AA404 - 419404 - 419
225SERSERLEULEU1BB404 - 419404 - 419
126LEULEUTYRTYR1AA421 - 445421 - 445
226LEULEUTYRTYR1BB421 - 445421 - 445
127GLUGLUGLUGLU3AA8484
227GLUGLUGLUGLU3BB8484
128ASNASNSERSER1AA85 - 13985 - 139
228ASNASNSERSER1BB85 - 13985 - 139
129THRTHRTHRTHR3AA457457
229THRTHRTHRTHR3BB457457
130LEULEUALAALA1AA458 - 465458 - 465
230LEULEUALAALA1BB458 - 465458 - 465
131HISHISHISHIS3AA140140
231HISHISHISHIS3BB140140

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

NCS oper: (Code: given
Matrix: (1, 0.00526, -0.001397), (0.005272, -0.9999, 0.009144), (-0.001349, -0.009151, -1)
Vector: -36.46, -33.48, -56.34)

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Components

#1: Protein MAN26A / BETA-1 / 4-MANNANASE


Mass: 50466.121 Da / Num. of mol.: 2 / Fragment: CATALYTIC AND IGG-LIKE DOMAIN, RESIDUES 52-514 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLULOMONAS FIMI (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9XCV5, mannan endo-1,4-beta-mannosidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 373 TO ARG ENGINEERED RESIDUE IN CHAIN A, PHE 375 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ALA 373 TO ARG ENGINEERED RESIDUE IN CHAIN A, PHE 375 TO ALA ENGINEERED RESIDUE IN CHAIN B, ALA 373 TO ARG ENGINEERED RESIDUE IN CHAIN B, PHE 375 TO ALA

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 5.9
Details: VAPOR DIFFUSION. PROTEIN SOLUTION (8.4 MG/ML) IN 50 MM SODIUM CITRATE BUFFER, PH 6.0. RESERVOIR CONDITIONS: 0.2 M MAGNESIUM FORMATE, PH 5.9, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Oct 30, 2008 / Details: MULTILAYER MIRROR
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 2.35→19.43 Å / Num. obs: 41120 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMVERSION 7.0.1data reduction
SCALA3.2.5data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVY
Resolution: 2.35→19.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.498 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19935 2065 5 %RANDOM
Rwork0.1579 ---
obs0.15997 38998 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.604 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 28 625 7429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.939684
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07623.939330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76115954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3311543
X-RAY DIFFRACTIONr_chiral_restr0.0740.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025587
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.23167
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24815
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4691.54611
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82127199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.03332855
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6354.52474
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A59tight positional0.020.05
12B59tight positional0.020.05
21A9tight positional00.05
22B9tight positional00.05
3232A736tight positional0.020.05
3232B736tight positional0.020.05
41A5tight positional00.05
42B5tight positional00.05
51A5tight positional0.010.05
52B5tight positional0.010.05
61A3tight positional0.010.05
62B3tight positional0.010.05
71A4tight positional0.010.05
72B4tight positional0.010.05
81A9tight positional0.010.05
82B9tight positional0.010.05
91A8tight positional00.05
92B8tight positional00.05
101A3tight positional00.05
102B3tight positional00.05
111A4tight positional0.020.05
112B4tight positional0.020.05
121A3tight positional0.020.05
122B3tight positional0.020.05
131A5tight positional00.05
141A4tight positional0.010.05
151A48tight positional0.020.05
152B48tight positional0.020.05
161A126tight positional0.020.05
162B126tight positional0.020.05
171A357tight positional0.020.05
172B357tight positional0.020.05
181A24tight positional0.020.05
182B24tight positional0.020.05
191A88tight positional0.020.05
192B88tight positional0.020.05
201A608tight positional0.020.05
202B608tight positional0.020.05
211A82tight positional0.020.05
212B82tight positional0.020.05
221A221tight positional0.020.05
231A104tight positional0.020.05
241A80tight positional0.020.05
242B80tight positional0.020.05
251A101tight positional0.020.05
252B101tight positional0.020.05
261A136tight positional0.020.05
262B136tight positional0.020.05
271A3tight positional0.010.05
272B3tight positional0.010.05
281A406tight positional0.020.05
282B406tight positional0.020.05
291A4tight positional0.020.05
292B4tight positional0.020.05
301A59tight positional0.020.05
302B59tight positional0.020.05
311A4tight positional0.010.05
312B4tight positional0.010.05
41A10loose positional0.145
42B10loose positional0.145
51A14loose positional1.455
52B14loose positional1.455
71A4loose positional0.935
72B4loose positional0.935
91A10loose positional0.165
92B10loose positional0.165
111A3loose positional1.055
112B3loose positional1.055
131A8loose positional0.265
141A3loose positional0.745
291A3loose positional0.15
292B3loose positional0.15
311A6loose positional0.745
312B6loose positional0.745
11A59tight thermal0.070.5
12B59tight thermal0.070.5
21A9tight thermal0.040.5
22B9tight thermal0.040.5
3232A736tight thermal0.060.5
3232B736tight thermal0.060.5
41A5tight thermal0.040.5
42B5tight thermal0.040.5
51A5tight thermal0.050.5
52B5tight thermal0.050.5
61A3tight thermal0.050.5
62B3tight thermal0.050.5
71A4tight thermal0.050.5
72B4tight thermal0.050.5
81A9tight thermal0.070.5
82B9tight thermal0.070.5
91A8tight thermal0.040.5
92B8tight thermal0.040.5
101A3tight thermal0.150.5
102B3tight thermal0.150.5
111A4tight thermal0.210.5
112B4tight thermal0.210.5
121A3tight thermal0.060.5
122B3tight thermal0.060.5
131A5tight thermal0.060.5
141A4tight thermal0.040.5
151A48tight thermal0.060.5
152B48tight thermal0.060.5
161A126tight thermal0.070.5
162B126tight thermal0.070.5
171A357tight thermal0.060.5
172B357tight thermal0.060.5
181A24tight thermal0.030.5
182B24tight thermal0.030.5
191A88tight thermal0.070.5
192B88tight thermal0.070.5
201A608tight thermal0.060.5
202B608tight thermal0.060.5
211A82tight thermal0.060.5
212B82tight thermal0.060.5
221A221tight thermal0.070.5
231A104tight thermal0.070.5
241A80tight thermal0.070.5
242B80tight thermal0.070.5
251A101tight thermal0.030.5
252B101tight thermal0.030.5
261A136tight thermal0.070.5
262B136tight thermal0.070.5
271A3tight thermal0.130.5
272B3tight thermal0.130.5
281A406tight thermal0.060.5
282B406tight thermal0.060.5
291A4tight thermal0.090.5
292B4tight thermal0.090.5
301A59tight thermal0.070.5
302B59tight thermal0.070.5
311A4tight thermal0.090.5
312B4tight thermal0.090.5
41A10loose thermal0.3210
42B10loose thermal0.3210
51A14loose thermal1.2210
52B14loose thermal1.2210
71A4loose thermal0.6510
72B4loose thermal0.6510
91A10loose thermal0.1610
92B10loose thermal0.1610
111A3loose thermal1.0410
112B3loose thermal1.0410
131A8loose thermal0.3210
141A3loose thermal0.1510
291A3loose thermal0.3910
292B3loose thermal0.3910
311A6loose thermal1.1310
312B6loose thermal1.1310
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 142 -
Rwork0.201 2855 -
obs--99.83 %

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Yorodumi

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  • 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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