[English] 日本語
Yorodumi
- PDB-3dtd: Crystal structure of invasion associated protein b from bartonell... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dtd
TitleCrystal structure of invasion associated protein b from bartonella henselae
ComponentsInvasion-associated protein B
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / INVASION ASSOCIATED PROTEIN / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homologyInvasion associated locus B (IalB) protein / Invasion protein B / Invasion protein B superfamily / Invasion associated locus B (IalB) protein / Immunoglobulin-like / Sandwich / Mainly Beta / Invasion-associated protein B / Invasion-associated protein B
Function and homology information
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsPatskovsky, Y. / Ozyurt, S. / Freeman, J. / Slocombe, A. / Groshong, C. / Koss, J. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. ...Patskovsky, Y. / Ozyurt, S. / Freeman, J. / Slocombe, A. / Groshong, C. / Koss, J. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Invasion Associated Protein B from Bartonella Henselae.
Authors: Patskovsky, Y. / Ozyurt, S. / Freeman, J. / Slocombe, A. / Groshong, C. / Koss, J. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Invasion-associated protein B
B: Invasion-associated protein B
C: Invasion-associated protein B
D: Invasion-associated protein B
E: Invasion-associated protein B
F: Invasion-associated protein B
G: Invasion-associated protein B
H: Invasion-associated protein B
I: Invasion-associated protein B
J: Invasion-associated protein B
K: Invasion-associated protein B
L: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,75830
Polymers226,10112
Non-polymers1,65818
Water7,494416
1
F: Invasion-associated protein B
hetero molecules

C: Invasion-associated protein B
D: Invasion-associated protein B
E: Invasion-associated protein B
G: Invasion-associated protein B
hetero molecules

A: Invasion-associated protein B
B: Invasion-associated protein B
H: Invasion-associated protein B
I: Invasion-associated protein B
J: Invasion-associated protein B
K: Invasion-associated protein B
L: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,75830
Polymers226,10112
Non-polymers1,65818
Water21612
TypeNameSymmetry operationNumber
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
crystal symmetry operation2_355-x-3/2,-y,z+1/21
identity operation1_555x,y,z1
Buried area21310 Å2
ΔGint-78 kcal/mol
Surface area83290 Å2
MethodPISA
2
F: Invasion-associated protein B
hetero molecules

G: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8684
Polymers37,6832
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x-1,y-1/2,-z-1/21
Buried area1670 Å2
ΔGint-6 kcal/mol
Surface area15360 Å2
MethodPISA
3
K: Invasion-associated protein B
L: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9605
Polymers37,6832
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-6 kcal/mol
Surface area15630 Å2
MethodPISA
4
H: Invasion-associated protein B
I: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1447
Polymers37,6832
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-7 kcal/mol
Surface area15530 Å2
MethodPISA
5
D: Invasion-associated protein B
hetero molecules

A: Invasion-associated protein B


Theoretical massNumber of molelcules
Total (without water)37,7763
Polymers37,6832
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_354-x-3/2,-y,z-1/21
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area15430 Å2
MethodPISA
6
C: Invasion-associated protein B
E: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0526
Polymers37,6832
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-5 kcal/mol
Surface area15630 Å2
MethodPISA
7
B: Invasion-associated protein B
J: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9605
Polymers37,6832
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-5 kcal/mol
Surface area15670 Å2
MethodPISA
8
A: Invasion-associated protein B


Theoretical massNumber of molelcules
Total (without water)18,8421
Polymers18,8421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
B: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0263
Polymers18,8421
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
C: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2105
Polymers18,8421
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
D: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9342
Polymers18,8421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
E: Invasion-associated protein B


Theoretical massNumber of molelcules
Total (without water)18,8421
Polymers18,8421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
F: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9342
Polymers18,8421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
G: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9342
Polymers18,8421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
H: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0263
Polymers18,8421
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
I: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1184
Polymers18,8421
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
J: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9342
Polymers18,8421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
K: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9342
Polymers18,8421
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
L: Invasion-associated protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0263
Polymers18,8421
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.707, 139.951, 179.075
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
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J
113K
123L
14A
24B
34C
44D
54E
64F
74G
84H
94I
104J
114K
124L

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERCYSAA42 - 5424 - 36
21SERCYSBB42 - 5424 - 36
31SERCYSCC42 - 5424 - 36
41SERCYSDD42 - 5424 - 36
51SERCYSEE42 - 5424 - 36
61SERCYSFF42 - 5424 - 36
71SERCYSGG42 - 5424 - 36
81SERCYSHH42 - 5424 - 36
91SERCYSII42 - 5424 - 36
101SERCYSJJ42 - 5424 - 36
111SERCYSKK42 - 5424 - 36
121SERCYSLL42 - 5424 - 36
12CYSVALAA63 - 8345 - 65
22CYSVALBB63 - 8345 - 65
32CYSVALCC63 - 8345 - 65
42CYSVALDD63 - 8345 - 65
52CYSVALEE63 - 8345 - 65
62CYSVALFF63 - 8345 - 65
72CYSVALGG63 - 8345 - 65
82CYSVALHH63 - 8345 - 65
92CYSVALII63 - 8345 - 65
102CYSVALJJ63 - 8345 - 65
112CYSVALKK63 - 8345 - 65
122CYSVALLL63 - 8345 - 65
13SERVALAA91 - 11073 - 92
23SERVALBB91 - 11073 - 92
33SERVALCC91 - 11073 - 92
43SERVALDD91 - 11073 - 92
53SERVALEE91 - 11073 - 92
63SERVALFF91 - 11073 - 92
73SERVALGG91 - 11073 - 92
83SERVALHH91 - 11073 - 92
93SERVALII91 - 11073 - 92
103SERVALJJ91 - 11073 - 92
113SERVALKK91 - 11073 - 92
123SERVALLL91 - 11073 - 92
14VALGLUAA116 - 18698 - 168
24VALGLUBB116 - 18698 - 168
34VALGLUCC116 - 18698 - 168
44VALGLUDD116 - 18698 - 168
54VALGLUEE116 - 18698 - 168
64VALGLUFF116 - 18698 - 168
74VALGLUGG116 - 18698 - 168
84VALGLUHH116 - 18698 - 168
94VALGLUII116 - 18698 - 168
104VALGLUJJ116 - 18698 - 168
114VALGLUKK116 - 18698 - 168
124VALGLULL116 - 18698 - 168

NCS ensembles :
ID
1
2
3
4
Detailsauthors states that the biological unit is likely monomer, PISA, however, suggests a possible dodecamer, listed in REMARK350

-
Components

#1: Protein
Invasion-associated protein B


Mass: 18841.729 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: invB, BH01650 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G4Y3, UniProt: A0A0H3LVG3*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200mM Trimethylamine N-oxide, 100MM TRIS-HCL, PH 8, 20% PEG MME 2000, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 8.00

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2008
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 100682 / % possible obs: 99.7 % / Observed criterion σ(I): -0.5 / Redundancy: 6.4 % / Biso Wilson estimate: 52.606 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 0.5 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
RESOLVEmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.208 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26524 3000 3 %RANDOM
Rwork0.23501 ---
obs0.23591 96697 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13106 0 108 416 13630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02213582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.97418441
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14851758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.924.695541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.548152346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9641583
X-RAY DIFFRACTIONr_chiral_restr0.0760.22202
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029941
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1310.34994
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.58845
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.51083
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.3101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.66228931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.345314047
X-RAY DIFFRACTIONr_scbond_it4.87935129
X-RAY DIFFRACTIONr_scangle_it7.71354375
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
11A103medium positional0.040.1
12B103medium positional0.040.1
13C103medium positional0.030.1
14D103medium positional0.040.1
15E103medium positional0.040.1
16F103medium positional0.030.1
17G103medium positional0.050.1
18H103medium positional0.040.1
19I103medium positional0.040.1
110J103medium positional0.030.1
111K103medium positional0.040.1
112L103medium positional0.030.1
21A151medium positional0.110.1
22B151medium positional0.040.1
23C151medium positional0.050.1
24D151medium positional0.050.1
25E151medium positional0.050.1
26F151medium positional0.050.1
27G151medium positional0.120.1
28H151medium positional0.040.1
29I151medium positional0.050.1
210J151medium positional0.040.1
211K151medium positional0.040.1
212L151medium positional0.040.1
31A138medium positional0.030.1
32B138medium positional0.040.1
33C138medium positional0.040.1
34D138medium positional0.030.1
35E138medium positional0.030.1
36F138medium positional0.040.1
37G138medium positional0.040.1
38H138medium positional0.030.1
39I138medium positional0.030.1
310J138medium positional0.040.1
311K138medium positional0.030.1
312L138medium positional0.030.1
41A510medium positional0.030.1
42B510medium positional0.040.1
43C510medium positional0.040.1
44D510medium positional0.040.1
45E510medium positional0.040.1
46F510medium positional0.040.1
47G510medium positional0.060.1
48H510medium positional0.040.1
49I510medium positional0.030.1
410J510medium positional0.040.1
411K510medium positional0.030.1
412L510medium positional0.030.1
11A103medium thermal0.291.5
12B103medium thermal0.281.5
13C103medium thermal0.371.5
14D103medium thermal0.281.5
15E103medium thermal0.261.5
16F103medium thermal0.261.5
17G103medium thermal0.281.5
18H103medium thermal0.291.5
19I103medium thermal0.291.5
110J103medium thermal0.291.5
111K103medium thermal0.31.5
112L103medium thermal0.261.5
21A151medium thermal0.241.5
22B151medium thermal0.361.5
23C151medium thermal0.321.5
24D151medium thermal0.321.5
25E151medium thermal0.251.5
26F151medium thermal0.281.5
27G151medium thermal0.261.5
28H151medium thermal0.271.5
29I151medium thermal0.251.5
210J151medium thermal0.261.5
211K151medium thermal0.311.5
212L151medium thermal0.331.5
31A138medium thermal0.261.5
32B138medium thermal0.221.5
33C138medium thermal0.261.5
34D138medium thermal0.251.5
35E138medium thermal0.251.5
36F138medium thermal0.251.5
37G138medium thermal0.221.5
38H138medium thermal0.221.5
39I138medium thermal0.231.5
310J138medium thermal0.271.5
311K138medium thermal0.231.5
312L138medium thermal0.251.5
41A510medium thermal0.261.5
42B510medium thermal0.271.5
43C510medium thermal0.31.5
44D510medium thermal0.221.5
45E510medium thermal0.211.5
46F510medium thermal0.261.5
47G510medium thermal0.221.5
48H510medium thermal0.231.5
49I510medium thermal0.251.5
410J510medium thermal0.261.5
411K510medium thermal0.261.5
412L510medium thermal0.261.5
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 187 -
Rwork0.341 6584 -
obs--93.28 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more