[English] 日本語
Yorodumi
- PDB-4urh: High-resolution structure of partially oxidized D. fructosovorans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4urh
TitleHigh-resolution structure of partially oxidized D. fructosovorans NiFe-hydrogenase
Components
  • HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
  • NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
KeywordsOXIDOREDUCTASE / NIFE-SITE / NI-SU STATE / SULFENATE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / 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 ...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
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Nickel-dependent hydrogenase large subunit / cytochrome-c3 hydrogenase / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO FRUCTOSOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsVolbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / DeLacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C.
Citation
Journal: J. Biol. Inorg. Chem. / Year: 2015
Title: Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.
Authors: Volbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / De Lacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C.
#1: 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.J. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
History
DepositionJun 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method
Revision 1.3Feb 27, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 10, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.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_alt_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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.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_type.id / _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_alt_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "RZ" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "RZ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,99330
Polymers268,8556
Non-polymers4,13924
Water36,4262022
1
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9289
Polymers89,6182
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-121.6 kcal/mol
Surface area25310 Å2
MethodPISA
2
A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,13712
Polymers89,6182
Non-polymers1,51910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-126.7 kcal/mol
Surface area25570 Å2
MethodPISA
3
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9289
Polymers89,6182
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-119.7 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.530, 99.820, 182.420
Angle α, β, γ (deg.)90.00, 92.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
12R

NCS domain segments:

Dom-ID: 1 / Refine code: 1

Component-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label alt-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLYAGLYBB3 - 2644 - 265
21SF4SF4SF4SF4BL - N1265 - 1267
12LYSLYSHISAHISRE5 - 54919 - 563
22FCOFCOGOLGOLRW - Z1550 - 1553

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 6 molecules ABCQRS

#1: Protein HYDROGENASE (NIFE) SMALL SUBUNIT HYDA / NIFE-HYDROGENASE SMALL SUBUNIT


Mass: 28418.389 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
References: UniProt: E1K248, UniProt: P18187*PLUS, cytochrome-c3 hydrogenase
#2: Protein NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / NIFE-HYDROGENASE LARGE SUBUNIT


Mass: 61199.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
References: UniProt: E1K247, UniProt: P18188*PLUS, cytochrome-c3 hydrogenase

-
Non-polymers , 7 types, 2046 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3FeN2O
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2022 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsN-TERMINAL STREP-TAG IN LARGE SUBUNIT ACTIVE SITE DETAILS: THE STRUCTURE PROBABLY CONTAINS 50% OF ...N-TERMINAL STREP-TAG IN LARGE SUBUNIT ACTIVE SITE DETAILS: THE STRUCTURE PROBABLY CONTAINS 50% OF THE UNREADY DIAMAGNETIC NI-SU STATE, WITH NI(II) BOUND TO CYS72-SG, CSX75-OD (SULFENATE), CYS543-SG, O2001 AND CYS546-SG IN A DISTORTED SQUARE PYRAMIDAL COORDINATION (CHAINS Q, R, AND S). THIS STATE IS ISOSTRUCTURAL WITH THE UNREADY PARAMAGNETIC NI-A STATE (WITH NI(III)). THE ACTIVE SITE STATES OF THE REMAINING 50% OF THE STRUCTURE, WHICH PARTIALLY INVOLVE A SECOND CONFOR- MATION OF CYS543, ARE NOT RESOLVED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: VAPOR DIFFUSION, GLOVE BOX, 298K, PEG6000, MES, HEPES, DTT, DITHIONITE, PH 6.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.44→29.8 Å / Num. obs: 400635 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.67 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.39
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.29 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw


Resolution: 1.44→25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.703 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WERE REFINED INDIVIDUALLY. TWO OVERLAPPING MOLECULAR REPLACEMENT SOLUTIONS WERE FOUND FOR ONE OF THE THREE HYDROGENASE HETERODIMERS IN THE ASYMMETRIC UNIT, CONSISTING OF SUBUNITS B ...Details: U VALUES WERE REFINED INDIVIDUALLY. TWO OVERLAPPING MOLECULAR REPLACEMENT SOLUTIONS WERE FOUND FOR ONE OF THE THREE HYDROGENASE HETERODIMERS IN THE ASYMMETRIC UNIT, CONSISTING OF SUBUNITS B AND R. THESE WERE REFINED WITH TIGHT NON -CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS AND WITH OCCUPANCIES OF 0.50 EACH. THE SECOND SOLUTION IS INCLUDED AS ALTERNATE CONFORMERS LABELLED X AND Y
RfactorNum. reflection% reflectionSelection details
Rfree0.18526 20075 5 %RANDOM
Rwork0.14164 ---
obs0.14381 380536 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.503 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20.28 Å2
2---0.38 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.44→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18454 0 127 2022 20603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01925940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.98435219
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74453265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04324.5211055
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.495154245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8291598
X-RAY DIFFRACTIONr_chiral_restr0.0910.23881
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02119550
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.0661.56612973
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3372.9416213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.21.75712986
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

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2003tight positional0.030.05
2R4197tight positional0.030.05
1B2003tight thermal3.930.5
2R4197tight thermal2.750.5
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 1439 -
Rwork0.288 26675 -
obs--94.76 %

+
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