[English] 日本語
Yorodumi
- PDB-1yqw: Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yqw
TitleStructure of the Oxidized Unready Form of Ni-Fe Hydrogenase
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / NI-FE HYDROGENASE UNREADY STATE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / : / NICKEL (II) ION / PEROXIDE ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio fructosovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsVolbeda, A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
#1: Journal: Int.J.Hydrogen Energy / Year: 2002
Title: High-Resolution Crystallographic Analysis of Desulfovibrio Fructosovorans [NiFe] Hydrogenase
Authors: Volbeda, A. / Montet, Y. / Vernede, X. / Hatchikian, E.C. / Fontecilla-Camps, J.C.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Gas Access to the Active Site of Ni-Fe Hydrogenases Probed by X-Ray Crystallography and Molecular Dynamics
Authors: Montet, Y. / Amara, P. / Volbeda, A. / Vernede, X. / Hatchikian, E.C. / Field, M.J. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionFeb 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Aug 31, 2011Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.6Aug 23, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_symmetry / _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: Periplasmic [NiFe] hydrogenase small subunit
Q: Periplasmic [NiFe] hydrogenase large subunit
B: Periplasmic [NiFe] hydrogenase small subunit
R: Periplasmic [NiFe] hydrogenase large subunit
C: Periplasmic [NiFe] hydrogenase small subunit
S: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,72648
Polymers264,1826
Non-polymers5,54442
Water33,2921848
1
A: Periplasmic [NiFe] hydrogenase small subunit
Q: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,09619
Polymers88,0612
Non-polymers2,03617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-144 kcal/mol
Surface area25000 Å2
MethodPISA, PQS
2
B: Periplasmic [NiFe] hydrogenase small subunit
R: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,01117
Polymers88,0612
Non-polymers1,95015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-136 kcal/mol
Surface area25120 Å2
MethodPISA, PQS
3
C: Periplasmic [NiFe] hydrogenase small subunit
S: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,61812
Polymers88,0612
Non-polymers1,55810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-130 kcal/mol
Surface area24920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.410, 99.700, 182.830
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211
Detailsheterodimer of small and large subunit

-
Components

-
Periplasmic [NiFe] hydrogenase ... , 2 types, 6 molecules ABCQRS

#1: Protein Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain


Mass: 28347.314 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P18187, cytochrome-c3 hydrogenase
#2: Protein Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 59713.312 Da / Num. of mol.: 3 / Mutation: S499A / Source method: isolated from a natural source / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P18188, cytochrome-c3 hydrogenase

-
Non-polymers , 10 types, 1890 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3FeN2O
#11: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1848 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 6000, glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 / Wavelength: 0.954 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 1998 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.83→35 Å / Num. all: 169544 / Num. obs: 169544 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.06 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.054 / Net I/σ(I): 11.8
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 3.01 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.255 / % possible all: 68.5

-
Processing

Software
NameVersionClassification
XDSdata scaling
CCP4data reduction
AMoREphasing
REFMAC5.2.0005refinement
ProDCdata collection
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRF

1frf


Resolution: 1.83→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.504 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: use of TLS parameters for large subunits + N-terminal and C-terminal domains of small subunits
RfactorNum. reflection% reflectionSelection details
Rfree0.18467 8483 5 %RANDOM
Rwork0.14628 ---
all0.14821 168613 --
obs0.14821 160130 83.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.5 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.791 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å21.18 Å2
2---0.86 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18394 0 211 1848 20453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02219175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.96825974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49952411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02124.395769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.446153017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2431573
X-RAY DIFFRACTIONr_chiral_restr0.080.22835
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214427
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.29965
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.213059
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.21835
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.646212366
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.082319315
X-RAY DIFFRACTIONr_scbond_it2.69937779
X-RAY DIFFRACTIONr_scangle_it3.51246578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.911 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.237 837 -
Rwork0.198 16160 -
obs--69.31 %
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)
10.6512-0.0705-0.31050.52410.04650.99740.00910.00070.08470.05080.0243-0.0289-0.10560.0178-0.03340.0262-0.0009-0.05210.0110.00450.078812.47214.7364.913
20.3633-0.0286-0.04180.5650.12010.6115-0.0253-0.0165-0.03890.12430.0163-0.01230.11550.00130.0090.04850.0044-0.04150.02130.00930.07218.204-6.90314.73
30.6091-0.1256-0.10750.5911-0.02120.9842-0.0791-0.0291-0.13930.09940.01260.16210.1444-0.14340.06650.0868-0.01080.02230.1120.01860.1766-38.8-46.19252.496
40.3958-0.0799-0.06250.49920.10030.7245-0.0436-0.0609-0.00170.07080.0534-0.0288-0.00610.1011-0.00980.05060.0179-0.03530.09990.00720.0952-19.011-33.02249.199
50.59790.1527-0.25251.053-0.011.5330.0318-0.021-0.05990.0615-0.08080.15460.1969-0.23080.0490.1028-0.0231-0.02730.1063-0.02720.1082-16.375.70961.322
60.46630.0858-0.19641.03640.1371.42160.0712-0.16040.04930.2157-0.08470.0001-0.00860.08070.01350.1179-0.0149-0.04190.1314-0.02010.0868-4.84919.21377.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 264
2X-RAY DIFFRACTION1A268 - 270
3X-RAY DIFFRACTION1A271 - 475
4X-RAY DIFFRACTION1Q565 - 568
5X-RAY DIFFRACTION2Q6 - 549
6X-RAY DIFFRACTION2A535 - 540
7X-RAY DIFFRACTION2Q572 - 941
8X-RAY DIFFRACTION3B3 - 264
9X-RAY DIFFRACTION3B1011 - 1165
10X-RAY DIFFRACTION3R1020 - 1111
11X-RAY DIFFRACTION4R6 - 549
12X-RAY DIFFRACTION4R1301 - 1303
13X-RAY DIFFRACTION4Q1034
14X-RAY DIFFRACTION4R1304 - 1308
15X-RAY DIFFRACTION4B1313 - 1626
16X-RAY DIFFRACTION4C271
17X-RAY DIFFRACTION5C5 - 264
18X-RAY DIFFRACTION5Q1035 - 1037
19X-RAY DIFFRACTION5C272 - 411
20X-RAY DIFFRACTION5R2039
21X-RAY DIFFRACTION5S2024 - 2155
22X-RAY DIFFRACTION6S6 - 549
23X-RAY DIFFRACTION6S2301
24X-RAY DIFFRACTION6S2311 - 2541
25X-RAY DIFFRACTION6C448 - 449

+
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