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- PDB-2zp8: The Nature of the TRAP:Anti-TRAP complex -

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Basic information

Entry
Database: PDB / ID: 2zp8
TitleThe Nature of the TRAP:Anti-TRAP complex
Components
  • Transcription attenuation protein mtrB
  • Tryptophan RNA-binding attenuator protein-inhibitory protein
KeywordsRNA BINDING PROTEIN/TRANSCRIPTION / PROTEIN-PROTEIN COMPLEX / TRANSCRIPTION / RNA-binding / Transcription regulation / RNA BINDING PROTEIN-TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding / cytoplasm
Similarity search - Function
Chaperone, DNAj Protein; Chain A / Chaperone, DNAj Protein; Chain A - #10 / Tryptophan RNA-binding attenuator protein inhibitory protein / Tryptophan RNA-binding attenuator protein inhibitory protein / TRAP-like / Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily / Heat shock protein DnaJ, cysteine-rich domain superfamily ...Chaperone, DNAj Protein; Chain A / Chaperone, DNAj Protein; Chain A - #10 / Tryptophan RNA-binding attenuator protein inhibitory protein / Tryptophan RNA-binding attenuator protein inhibitory protein / TRAP-like / Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily / Heat shock protein DnaJ, cysteine-rich domain superfamily / Other non-globular / Special / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRYPTOPHAN / Tryptophan RNA-binding attenuator protein inhibitory protein / Transcription attenuation protein MtrB
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWatanabe, M. / Heddle, J.G. / Unzai, S. / Akashi, S. / Park, S.Y. / Tame, J.R.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The nature of the TRAP-Anti-TRAP complex.
Authors: Watanabe, M. / Heddle, J.G. / Kikuchi, K. / Unzai, S. / Akashi, S. / Park, S.Y. / Tame, J.R.
History
DepositionJul 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
D: Transcription attenuation protein mtrB
E: Tryptophan RNA-binding attenuator protein-inhibitory protein
F: Tryptophan RNA-binding attenuator protein-inhibitory protein
G: Tryptophan RNA-binding attenuator protein-inhibitory protein
H: Tryptophan RNA-binding attenuator protein-inhibitory protein
I: Tryptophan RNA-binding attenuator protein-inhibitory protein
J: Tryptophan RNA-binding attenuator protein-inhibitory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,17220
Polymers66,96310
Non-polymers1,20910
Water00
1
A: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
D: Transcription attenuation protein mtrB
E: Tryptophan RNA-binding attenuator protein-inhibitory protein
F: Tryptophan RNA-binding attenuator protein-inhibitory protein
G: Tryptophan RNA-binding attenuator protein-inhibitory protein
H: Tryptophan RNA-binding attenuator protein-inhibitory protein
I: Tryptophan RNA-binding attenuator protein-inhibitory protein
J: Tryptophan RNA-binding attenuator protein-inhibitory protein
hetero molecules

A: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
D: Transcription attenuation protein mtrB
E: Tryptophan RNA-binding attenuator protein-inhibitory protein
F: Tryptophan RNA-binding attenuator protein-inhibitory protein
G: Tryptophan RNA-binding attenuator protein-inhibitory protein
H: Tryptophan RNA-binding attenuator protein-inhibitory protein
I: Tryptophan RNA-binding attenuator protein-inhibitory protein
J: Tryptophan RNA-binding attenuator protein-inhibitory protein
hetero molecules

A: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
D: Transcription attenuation protein mtrB
E: Tryptophan RNA-binding attenuator protein-inhibitory protein
F: Tryptophan RNA-binding attenuator protein-inhibitory protein
G: Tryptophan RNA-binding attenuator protein-inhibitory protein
H: Tryptophan RNA-binding attenuator protein-inhibitory protein
I: Tryptophan RNA-binding attenuator protein-inhibitory protein
J: Tryptophan RNA-binding attenuator protein-inhibitory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,51760
Polymers200,88930
Non-polymers3,62830
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area67680 Å2
ΔGint-349 kcal/mol
Surface area72020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.134, 201.134, 133.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H
52I
62J
13E
23F
33G
43H
53I
63J
14E
24F
34G
44H
54I
64J

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALILEILEAA10 - 708 - 68
21VALVALILEILEBB10 - 708 - 68
31VALVALILEILECC10 - 708 - 68
41VALVALILEILEDD10 - 708 - 68
12METMETGLUGLUEE1 - 91 - 9
22METMETGLUGLUFF1 - 91 - 9
32METMETGLUGLUGG1 - 91 - 9
42METMETGLUGLUHH1 - 91 - 9
52METMETGLUGLUII1 - 91 - 9
62METMETGLUGLUJJ1 - 91 - 9
13VALVALILEILEEE10 - 3510 - 35
23VALVALILEILEFF10 - 3510 - 35
33VALVALILEILEGG10 - 3510 - 35
43VALVALILEILEHH10 - 3510 - 35
53VALVALILEILEII10 - 3510 - 35
63VALVALILEILEJJ10 - 3510 - 35
14LEULEULYSLYSEE36 - 5336 - 53
24LEULEULYSLYSFF36 - 5336 - 53
34LEULEULYSLYSGG36 - 5336 - 53
44LEULEULYSLYSHH36 - 5336 - 53
54LEULEULYSLYSII36 - 5336 - 53
64LEULEULYSLYSJJ36 - 5336 - 53

NCS ensembles :
ID
1
2
3
4
DetailsTHIS PDB FILE SHOWS THE COMPLEX BETWEEN WILD-TYPE BACILLUS STEAROTHERMOPHILUS TRAP AND BACILLUS SUBTILIS ANTI-TRAP. THE TRAP RING HAS SPONTANEOUSLY SHIFTED TO A 12-MER RING FROM THE USUAL 11-MER FORM. SOLUTION EXPERIMENTS SHOW THIS 12-MER RING FORM TO BE A MINOR SPECIES, HOWEVER, MUTATIONAL ANALYSIS INDICATES THE TRAP:ANTI-TRAP INTERFACE TO BE THE SAME AS THAT MADE BY 11-MER TRAP.

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Components

#1: Protein
Transcription attenuation protein mtrB / Tryptophan RNA-binding attenuator protein / Trp RNA-binding attenuation protein / TRAP


Mass: 8257.377 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Gene: mtrB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X6J6
#2: Protein
Tryptophan RNA-binding attenuator protein-inhibitory protein / Anti-TRAP protein / AT


Mass: 5655.565 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rtpA, yczA, BSU02530 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31466
#3: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M bicine pH 9.0, 10-13% PEG 10000, 2% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 27, 2007
RadiationMonochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 13867 / % possible obs: 81.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.072
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 1.6 / Num. unique all: 910 / Rsym value: 0.217 / % possible all: 53.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BX9, 1QAW
Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.857 / SU B: 42.047 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 718 5.2 %RANDOM
Rwork0.22869 ---
obs0.23067 13074 80.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.012 Å2
Baniso -1Baniso -2Baniso -3
1--4.71 Å2-2.36 Å20 Å2
2---4.71 Å20 Å2
3---7.07 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 66 0 4559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224587
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9686193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78624.759187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95115805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.111522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023392
X-RAY DIFFRACTIONr_nbd_refined0.2210.22060
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.213
X-RAY DIFFRACTIONr_mcbond_it0.221.53027
X-RAY DIFFRACTIONr_mcangle_it0.37424728
X-RAY DIFFRACTIONr_scbond_it0.731720
X-RAY DIFFRACTIONr_scangle_it1.2124.51465
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A244tight positional0.030.05
12B244tight positional0.030.05
13C244tight positional0.040.05
14D244tight positional0.030.05
21E36tight positional0.050.05
22F36tight positional0.050.05
23G36tight positional0.040.05
24H36tight positional0.050.05
25I36tight positional0.040.05
26J36tight positional0.030.05
31E104tight positional0.030.05
32F104tight positional0.030.05
33G104tight positional0.030.05
34H104tight positional0.020.05
35I104tight positional0.020.05
36J104tight positional0.040.05
41E72tight positional0.030.05
42F72tight positional0.030.05
43G72tight positional0.030.05
44H72tight positional0.030.05
45I72tight positional0.030.05
46J72tight positional0.030.05
11A222loose positional0.345
12B222loose positional0.295
13C222loose positional0.385
14D222loose positional0.365
21E32loose positional1.015
22F32loose positional0.785
23G32loose positional0.85
24H32loose positional0.925
25I32loose positional0.85
26J32loose positional0.765
31E71loose positional0.65
32F71loose positional0.385
33G71loose positional0.415
34H71loose positional0.55
35I71loose positional0.425
36J71loose positional0.355
41E77loose positional1.115
42F77loose positional0.875
43G77loose positional0.775
44H77loose positional1.015
45I77loose positional0.755
46J77loose positional0.825
11A244tight thermal0.050.5
12B244tight thermal0.050.5
13C244tight thermal0.050.5
14D244tight thermal0.050.5
21E36tight thermal0.040.5
22F36tight thermal0.040.5
23G36tight thermal0.040.5
24H36tight thermal0.050.5
25I36tight thermal0.040.5
26J36tight thermal0.040.5
31E104tight thermal0.020.5
32F104tight thermal0.030.5
33G104tight thermal0.040.5
34H104tight thermal0.020.5
35I104tight thermal0.020.5
36J104tight thermal0.030.5
41E72tight thermal0.040.5
42F72tight thermal0.030.5
43G72tight thermal0.030.5
44H72tight thermal0.030.5
45I72tight thermal0.030.5
46J72tight thermal0.040.5
11A222loose thermal0.6610
12B222loose thermal0.8910
13C222loose thermal0.9110
14D222loose thermal0.8910
21E32loose thermal1.1310
22F32loose thermal0.7510
23G32loose thermal0.5710
24H32loose thermal0.5710
25I32loose thermal0.7310
26J32loose thermal0.7610
31E71loose thermal0.5610
32F71loose thermal0.4210
33G71loose thermal0.3810
34H71loose thermal0.210
35I71loose thermal0.5510
36J71loose thermal0.6110
41E77loose thermal0.6810
42F77loose thermal0.610
43G77loose thermal0.7510
44H77loose thermal0.7210
45I77loose thermal0.4510
46J77loose thermal0.7610
LS refinement shellResolution: 3.204→3.285 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 35 -
Rwork0.252 621 -
obs-718 53.51 %
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)
10.8743-0.767-0.05491.90730.03740.5312-0.03330.1685-0.0646-0.1654-0.00580.1767-0.0249-0.06430.0391-0.2865-0.0512-0.0462-0.2498-0.02190.0358-22.923-9.461449.8323
216.19365.9353.284713.55071.742113.3275-1.13072.5723-0.5456-3.16560.6744-1.5602-0.88770.79680.45630.4061-0.02260.09910.1522-0.40640.4693-17.1059-40.529429.4012
34.18697.7126-2.14934.0384-1.8451.3282-0.28870.9256-0.4627-1.90690.26253.96350.2788-0.07810.0262-0.0097-0.0629-0.27720.1522-0.30360.7707-34.5552-48.62737.3922
45.1813-2.08520.413914.5021.680.28260.1350.55370.25-0.90210.15971.3066-0.5804-0.4538-0.2947-0.0036-0.0175-0.2570.1304-0.00440.3812-31.2149-29.336538.3056
517.2117-0.61640.69818.73070.378412.9051-0.09863.0113-0.4958-1.8795-0.3726-0.1450.28480.77870.47120.2714-0.1809-0.30960.3190.00530.6625-43.7355-5.566629.522
612.4625-1.6362-4.01681.52381.7282.396-0.21831.65230.6211-0.91420.16481.5137-0.28-0.98250.05350.2180.0369-0.42960.34030.04180.959-59.51745.731937.163
711.48785.72162.022611.94042.82250.7185-0.15190.8541.3167-1.69190.04181.4777-0.74540.39030.11010.33330.0187-0.4098-0.04940.23910.4488-40.965412.386738.1252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 708 - 68
2X-RAY DIFFRACTION1BB10 - 708 - 68
3X-RAY DIFFRACTION1CC10 - 708 - 68
4X-RAY DIFFRACTION1DD10 - 708 - 68
5X-RAY DIFFRACTION2EE1 - 91 - 9
6X-RAY DIFFRACTION2EE36 - 5336 - 53
7X-RAY DIFFRACTION2EE10 - 3510 - 35
8X-RAY DIFFRACTION2EL541
9X-RAY DIFFRACTION3FF1 - 91 - 9
10X-RAY DIFFRACTION3FF36 - 5336 - 53
11X-RAY DIFFRACTION3FF10 - 3510 - 35
12X-RAY DIFFRACTION3FM541
13X-RAY DIFFRACTION4GG1 - 91 - 9
14X-RAY DIFFRACTION4GG36 - 5336 - 53
15X-RAY DIFFRACTION4GG10 - 3510 - 35
16X-RAY DIFFRACTION4GN541
17X-RAY DIFFRACTION5HH1 - 91 - 9
18X-RAY DIFFRACTION5HH36 - 5336 - 53
19X-RAY DIFFRACTION5HH10 - 3510 - 35
20X-RAY DIFFRACTION5HO541
21X-RAY DIFFRACTION6II1 - 91 - 9
22X-RAY DIFFRACTION6II36 - 5336 - 53
23X-RAY DIFFRACTION6II10 - 3510 - 35
24X-RAY DIFFRACTION6IP541
25X-RAY DIFFRACTION7JJ1 - 91 - 9
26X-RAY DIFFRACTION7JJ36 - 5336 - 53
27X-RAY DIFFRACTION7JJ10 - 3510 - 35
28X-RAY DIFFRACTION7JK541

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