[English] 日本語
Yorodumi
- PDB-4urr: Tailspike protein of Sf6 bacteriophage bound to Shigella flexneri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4urr
TitleTailspike protein of Sf6 bacteriophage bound to Shigella flexneri O- antigen octasaccharide fragment
ComponentsBIFUNCTIONAL TAIL PROTEIN
KeywordsHYDROLASE / CARBOHYDRATE INTERACTION / TAILSPIKE PROTEIN / BETA HELIX
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / virion attachment to host cell
Similarity search - Function
: / Tailspike protein, C-terminal / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold ...: / Tailspike protein, C-terminal / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Tail spike protein
Similarity search - Component
Biological speciesSHIGELLA PHAGE SF6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGohlke, U. / Heinemann, U. / Seckler, R. / Barbirz, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2016
Title: Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions.
Authors: Kang, Y. / Gohlke, U. / Engstrom, O. / Hamark, C. / Scheidt, T. / Kunstmann, S. / Heinemann, U. / Widmalm, G. / Santer, M. / Barbirz, S.
#1: Journal: Structure / Year: 2008
Title: An Intersubunit Active Site between Supercoiled Parallel Beta Helices in the Trimeric Tailspike Endorhamnosidase of Shigella Flexneri Phage Sf6.
Authors: Muller, J.J. / Barbirz, S. / Heinle, K. / Freiberg, A. / Seckler, R. / Heinemann, U.
History
DepositionJul 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_database_status / struct_conn
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BIFUNCTIONAL TAIL PROTEIN
B: BIFUNCTIONAL TAIL PROTEIN
C: BIFUNCTIONAL TAIL PROTEIN
D: BIFUNCTIONAL TAIL PROTEIN
E: BIFUNCTIONAL TAIL PROTEIN
F: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,62931
Polymers329,5826
Non-polymers9,04725
Water27,7251539
1
A: BIFUNCTIONAL TAIL PROTEIN
B: BIFUNCTIONAL TAIL PROTEIN
C: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,28415
Polymers164,7913
Non-polymers4,49312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29750 Å2
ΔGint-12.1 kcal/mol
Surface area44650 Å2
MethodPISA
2
D: BIFUNCTIONAL TAIL PROTEIN
E: BIFUNCTIONAL TAIL PROTEIN
F: BIFUNCTIONAL TAIL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,34616
Polymers164,7913
Non-polymers4,55513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29860 Å2
ΔGint-3.9 kcal/mol
Surface area44720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.987, 138.895, 136.073
Angle α, β, γ (deg.)90.00, 92.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.315701, 0.058398, 0.94706), (0.930904, -0.21231, -0.297224), (0.183713, 0.975456, -0.121389)-13.355, 43.091, -18.412
2given(0.323051, 0.929802, 0.176368), (0.049659, -0.202758, 0.977969), (0.945078, -0.307176, -0.111674)-32.611, 27.503, 23.388
3given(0.331436, 0.929379, 0.162497), (0.013805, -0.17699, 0.984116), (0.943377, -0.323928, -0.071491)-30.385, 35.496, -43.608
4given(0.999933, -0.008693, 0.007645), (0.009041, 0.998868, -0.046698), (-0.00723, 0.046764, 0.99888)2.185, 9.513, -68.584
5given(0.311988, 0.070174, 0.947491), (0.925013, -0.250033, -0.286068), (0.216829, 0.965691, -0.142919)-11.715, 53.129, -84.76

-
Components

-
Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
BIFUNCTIONAL TAIL PROTEIN / TAILSPIKE-PROTEIN / TSP / ENDORHAMNOSIDASE / ENDO-1 / 3-ALPHA-L-RHAMNOSIDASE


Mass: 54930.371 Da / Num. of mol.: 6 / Fragment: ENDORHAMNOSIDASE DOMAIN, RESIDUES 110-623 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA PHAGE SF6 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9XJP3, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide
alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose- ...alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 1301.246 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-3DGlcpNAcb1-2LRhapa1-2LRhapa1-3LRhapa1-3DGlcpNAcb1-2LRhapa1-2LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a2211m-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2-1-1-1-2-1/a2-b1_b2-c1_c3-d1_d3-e1_e2-f1_f2-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(2+1)][a-L-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{[(3+1)][a-L-Rhap]{[(2+1)][a-L-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{}}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 1558 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1539 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsALPHA-L-RHAMNOSE (RAM): RAM IS PART OF THE OCTASACCHARIDE LIGAND N-ACETYL-D-GLUCOSAMINE (NAG): NAG ...ALPHA-L-RHAMNOSE (RAM): RAM IS PART OF THE OCTASACCHARIDE LIGAND N-ACETYL-D-GLUCOSAMINE (NAG): NAG IS PART OF THE OCTASACCHARIDE LIGAND

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.97 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLISED FROM 0.1 M MES, PH 6.5, 16 % PEG 8000, 20 MM MNCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→46.3 Å / Num. obs: 224609 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 14.29 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 6.2
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VBK

2vbk


Resolution: 1.95→45.33 Å / Cor.coef. Fo:Fc: 0.8972 / Cor.coef. Fo:Fc free: 0.8545 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.154
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=48267. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=48267. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=10.
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 11044 4.94 %RANDOM
Rwork0.1957 ---
obs0.1977 223380 99.87 %-
Displacement parametersBiso mean: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.5848 Å20 Å2-0.7726 Å2
2---2.1176 Å20 Å2
3---1.5328 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22868 0 584 1539 24991
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0147181HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1684877HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10444SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes601HARMONIC2
X-RAY DIFFRACTIONt_gen_planes7081HARMONIC5
X-RAY DIFFRACTIONt_it47181HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion14.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3395SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact51566SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2629 763 4.64 %
Rwork0.2204 15690 -
all0.2224 16453 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40690.06430.1820.05870.06030.12350.00210.0505-0.03320.0073-0.0124-0.02640.0287-0.00350.0103-0.0549-0.003-0.0725-0.00930.0102-0.00923.363719.708514.5415
20.31470.10230.17010.12590.14120.1494-0.00460.07370.0402-0.0351-0.0093-0.02380.0086-0.00120.0139-0.0681-0.0476-0.08780.03380.0907-0.00832.019537.4832-0.6901
30.45320.03410.11770.02230.04630.0979-0.00860.04510.0718-0.0034-0.0242-0.016-0.006-0.02220.0329-0.06740.0032-0.0792-0.02850.04070.0232-11.042837.640318.673
40.20220.10840.18310.25540.15740.27270.0103-0.07860.0290.02590.03260.0072-0.0269-0.019-0.0428-0.0435-0.0214-0.02470.0087-0.0876-0.0107-8.891646.1335-48.0407
50.5080.04170.28130.01620.01490.37050.0175-0.0866-0.02920.0164-0.00120.024-0.01380.0583-0.0163-0.0343-0.0023-0.07680.0129-0.0172-0.03094.971128.3217-53.6957
60.38510.0807-0.03490.1098-0.02960.04310.012-0.02990.0686-0.00830.0218-0.0249-0.0415-0.0041-0.0338-0.0764-0.0001-0.0531-0.0322-0.07530.03763.978946.8366-67.3937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

+
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://pdbjlvh1.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