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- PDB-3zmd: Crystal structure of AbsC, a MarR family transcriptional regulato... -

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Basic information

Entry
Database: PDB / ID: 3zmd
TitleCrystal structure of AbsC, a MarR family transcriptional regulator from Streptomyces coelicolor
ComponentsPUTATIVE TRANSCRIPTIONAL REGULATORTranscriptional regulation
KeywordsTRANSCRIPTION / MARR-FAMILY / WINGED HELIX MOTIF
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Putative transcriptional regulator
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.95 Å
AuthorsStevenson, C.E.M. / Kock, H. / Mootien, S. / Davies, S.C. / Bibb, M.J. / Lawson, D.M.
Citation
Journal: To be Published
Title: Crystal Structure of Absc, a Marr Family Transcriptional Regulator from Streptomyces Coelicolor
Authors: Stevenson, C.E.M. / Kock, H. / Mootien, S. / Davies, S.C. / Bibb, M.J. / Lawson, D.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and Preliminary X-Ray Analysis of Absc, a Novel Regulator of Antibiotic Production in Streptomyces Coelicolor.
Authors: Stevenson, C.E.M. / Kock, H. / Mootien, S. / Davies, S.C. / Bibb, M.J. / Lawson, D.M.
History
DepositionFeb 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: 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_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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _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: PUTATIVE TRANSCRIPTIONAL REGULATOR
B: PUTATIVE TRANSCRIPTIONAL REGULATOR
C: PUTATIVE TRANSCRIPTIONAL REGULATOR
D: PUTATIVE TRANSCRIPTIONAL REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,76618
Polymers82,0574
Non-polymers70914
Water6,179343
1
A: PUTATIVE TRANSCRIPTIONAL REGULATOR
B: PUTATIVE TRANSCRIPTIONAL REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,53211
Polymers41,0282
Non-polymers5039
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-39.7 kcal/mol
Surface area15460 Å2
MethodPISA
2
C: PUTATIVE TRANSCRIPTIONAL REGULATOR
D: PUTATIVE TRANSCRIPTIONAL REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2347
Polymers41,0282
Non-polymers2065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-57.7 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.648, 120.483, 144.290
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
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA7 - 15427 - 174
21GLNGLNBB7 - 15427 - 174
12GLYGLYAA7 - 15327 - 173
22GLYGLYCC7 - 15327 - 173
13GLNGLNAA7 - 15427 - 174
23GLNGLNDD7 - 15427 - 174
14GLYGLYBB7 - 15327 - 173
24GLYGLYCC7 - 15327 - 173
15GLNGLNBB7 - 15427 - 174
25GLNGLNDD7 - 15427 - 174
16GLYGLYCC7 - 15327 - 173
26GLYGLYDD7 - 15327 - 173

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PUTATIVE TRANSCRIPTIONAL REGULATOR / Transcriptional regulation / ABSC


Mass: 20514.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A TWENTY RESIDUE HIS-TAG WAS APPENDED AT THE N-TERMINUS OF THE WILD-TYPE SEQUENCE, BUT THIS WAS NOT VISIBLE IN THE ELECTRON DENSITY. RESIDUE NUMBERING IS RELATIVE TO THE FULL-LENGTH WILD-TYPE SEQUENCE.
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: M145 / Plasmid: PET15B-ABSC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9L2B5

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details2-HYDROXYBENZOIC ACID (SAL): SALICYLATE WAS NOT DELIBERATELY ADDED TO THE PROTEIN AT ANY STAGE, BUT ...2-HYDROXYBENZOIC ACID (SAL): SALICYLATE WAS NOT DELIBERATELY ADDED TO THE PROTEIN AT ANY STAGE, BUT THIS LIGAND WAS CONSISTENT WITH THE OBSERVED ELECTRON DENSITY.

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 5.6 / Details: SEE REFERENCE 1., pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.49
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49 Å / Relative weight: 1
ReflectionResolution: 1.95→48.11 Å / Num. obs: 56091 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.95→44.68 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.337 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24282 2794 5 %RANDOM
Rwork0.21477 ---
obs0.21617 53215 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.32 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 41 343 5096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194958
X-RAY DIFFRACTIONr_bond_other_d0.0080.023402
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9516721
X-RAY DIFFRACTIONr_angle_other_deg1.58338264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8015626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07823.425254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6951553
X-RAY DIFFRACTIONr_chiral_restr0.0850.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025527
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021026
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A48950.16
12B48950.16
21A48420.15
22C48420.15
31A50330.14
32D50330.14
41B48770.16
42C48770.16
51B50070.14
52D50070.14
61C49790.13
62D49790.13
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 196 -
Rwork0.426 3608 -
obs--98.5 %
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)
111.8123-10.39627.353113.179-5.50737.28210.11810.4789-0.1122-0.4461-0.28910.01380.03950.27120.1710.1138-0.04450.00590.0704-0.01460.031213.419751.858357.4542
29.07647.58422.698611.6245-1.04854.55890.12150.0156-0.4579-0.5068-0.0752-0.11530.59-0.1207-0.04630.25650.03550.01210.14480.03340.110710.64278.151548.5975
312.3544-2.76933.03483.5171-0.94493.7636-0.02150.3998-0.5473-0.4669-0.056-0.13510.80640.23210.07750.33740.04420.0880.1845-0.00810.16417.670177.130941.8726
40.9751.699-1.7944.367-3.62843.49010.1287-0.06610.155-0.08240.09020.1239-0.16060.0397-0.21880.1846-0.02460.00270.1589-0.01860.07278.652277.423252.7418
525.04130.4655-19.75046.95132.958431.59790.2066-1.13550.6277-0.1943-0.1488-0.334-1.33380.7276-0.05790.08820.0029-0.02410.16750.02910.139221.595364.347763.7928
611.0972-9.3433-7.59310.64317.23016.75040.33880.54070.2318-0.4431-0.3518-0.135-0.3238-0.3230.01310.1293-0.01330.01510.09670.06550.073813.030467.422958.2375
74.08270.96960.09742.86050.54693.69830.0721-0.06570.58630.0406-0.03580.3133-0.3572-0.365-0.03630.16770.054-0.01250.0833-0.00120.142310.948145.054344.4214
819.36545.3155-1.90082.733-3.03095.1338-0.31970.6050.1747-0.33110.42210.09910.4731-0.5543-0.10240.27960.0268-0.0090.11740.05110.076912.244140.375735.9135
90.51570.93251.54233.34632.68194.67170.0704-0.1098-0.01450.0157-0.0854-0.11230.2171-0.25120.0150.06370.00770.00830.17030.0740.056617.37743.868152.3656
1015.1420.71677.31877.2062-0.586626.44950.1322-0.2821-0.6489-0.2732-0.080.22180.9458-0.0687-0.05220.082-0.0006-0.05780.068-0.02230.13573.325954.656961.534
118.0331-7.36525.15849.2842-4.68424.29140.25850.4252-0.1368-0.493-0.18440.21070.27120.2239-0.0740.0982-0.012-0.00220.1099-0.0210.045411.2016115.26658.5427
124.64240.79370.72124.5199-0.05264.13290.01750.0816-0.6529-0.0604-0.0291-0.34480.48770.04720.01160.1976-0.00750.04780.08210.03040.142413.6193137.12845.2968
1321.801912.30655.506316.39020.07489.8593-0.5857-0.28490.17610.06870.1664-0.7359-0.34760.47160.41930.32180.04020.06690.1760.00620.120722.4574146.720139.9761
141.0791.5762-2.24365.7477-5.28775.86930.0675-0.05370.12920.39310.22320.2425-0.3773-0.0639-0.29070.13670.0126-0.01460.1073-0.01180.02563.8423135.238257.3365
1514.81321.7778-4.61687.034-2.388217.53940.023-0.59790.7299-0.04510.1528-0.1631-0.94510.6844-0.17580.1243-0.0175-0.0150.0894-0.00080.111422.645126.668363.5676
1613.1147-10.7542-8.226211.74046.92737.210.08380.27530.2243-0.2646-0.0603-0.0823-0.144-0.1966-0.02360.1137-0.0196-0.0120.04960.03160.029412.7246129.07559.5267
174.00040.2955-1.06883.907-0.05934.14890.1532-0.13290.31310.1015-0.1750.4816-0.3233-0.30880.02180.15330.0376-0.01970.1097-0.060.136311.6888105.23646.0419
1831.32558.10245.67833.51552.18854.0472-0.055-0.2741-0.7270.0308-0.02740.24280.1153-0.47620.08240.13250.01810.01280.08840.01970.14769.882495.689643.5729
192.5779-0.59480.22314.15783.02426.8540.01360.0556-0.18440.03810.2288-0.21850.2420.1471-0.24240.01070.007-0.00360.1007-0.00120.034223.7662111.75761.7917
2026.57191.732919.81235.37920.19929.24890.2088-0.9665-0.5429-0.0776-0.09580.46860.9648-0.322-0.1130.0630.01510.04170.13430.02480.16153.5697116.633965.5651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 34
2X-RAY DIFFRACTION2A35 - 61
3X-RAY DIFFRACTION3A62 - 90
4X-RAY DIFFRACTION4A91 - 138
5X-RAY DIFFRACTION5A139 - 154
6X-RAY DIFFRACTION6B7 - 35
7X-RAY DIFFRACTION7B36 - 81
8X-RAY DIFFRACTION8B82 - 94
9X-RAY DIFFRACTION9B95 - 139
10X-RAY DIFFRACTION10B140 - 154
11X-RAY DIFFRACTION11C6 - 38
12X-RAY DIFFRACTION12C39 - 89
13X-RAY DIFFRACTION13C90 - 101
14X-RAY DIFFRACTION14C102 - 139
15X-RAY DIFFRACTION15C140 - 154
16X-RAY DIFFRACTION16D7 - 35
17X-RAY DIFFRACTION17D36 - 89
18X-RAY DIFFRACTION18D90 - 113
19X-RAY DIFFRACTION19D114 - 138
20X-RAY DIFFRACTION20D139 - 154

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