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- PDB-1yq9: Structure of the unready oxidized form of [NiFe] hydrogenase -

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Basic information

Entry
Database: PDB / ID: 1yq9
TitleStructure of the unready oxidized form of [NiFe] hydrogenase
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE
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 / 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 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 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 / HYDROSULFURIC ACID / NICKEL (II) ION / PEROXIDE ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVolbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
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: J.Am.Chem.Soc. / Year: 1996
Title: Structure of the [NiFe] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands
Authors: Volbeda, A. / Garcin, E. / Piras, C. / De Lacey, A.L. / Fernandez, V.M. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C.
#2: Journal: Nature / Year: 1995
Title: Crystal Structure of the nickel-iron hydrogenase from Desulfovibrio gigas
Authors: Volbeda, A. / Charon, M.H. / Piras, C. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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_ncs_dom_lim / struct_ref_seq_dif / 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_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_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_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.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ref_seq_dif.details / _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: Periplasmic [NiFe] hydrogenase small subunit
H: Periplasmic [NiFe] hydrogenase large subunit
B: Periplasmic [NiFe] hydrogenase small subunit
I: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,30029
Polymers176,0194
Non-polymers3,28125
Water9,278515
1
A: Periplasmic [NiFe] hydrogenase small subunit
H: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,88017
Polymers88,0092
Non-polymers1,87115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-137 kcal/mol
Surface area24970 Å2
MethodPISA
2
B: Periplasmic [NiFe] hydrogenase small subunit
I: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,42012
Polymers88,0092
Non-polymers1,41010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-135 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.750, 93.440, 69.030
Angle α, β, γ (deg.)89.33, 102.41, 90.95
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
12H
22I
32H
42I
52H
62I
72H
82I
92H
102I
112H
122I
132H
142I
152H
162I
172H
182I
192H
202I
212H
222I
232H
242I
252H
262I
272H
282I
292H
302I
312H
322I
332H
342I
352H
362I
372H
382I
392H
402I
412H
422I
432H
442I

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALASERSERAA15 - 2315 - 23
211ALAALASERSERBC15 - 2315 - 23
321GLUGLUGLYGLYAA73 - 7573 - 75
421GLUGLUGLYGLYBC73 - 7573 - 75
531ILEILEALAALAAA109 - 113109 - 113
631ILEILEALAALABC109 - 113109 - 113
741GLYGLYGLNGLNAA116 - 119116 - 119
841GLYGLYGLNGLNBC116 - 119116 - 119
951GLYGLYPROPROAA147 - 150147 - 150
1051GLYGLYPROPROBC147 - 150147 - 150
1161VALVALVALVALAA184184
1261VALVALVALVALBC184184
1371LYSLYSGLYGLYAA220 - 221220 - 221
1471LYSLYSGLYGLYBC220 - 221220 - 221
1581THRTHRTHRTHRAA224224
1681THRTHRTHRTHRBC224224
1791ASNASNPROPROAA226 - 229226 - 229
1891ASNASNPROPROBC226 - 229226 - 229
19101PHEPHEPHEPHEAA233233
20101PHEPHEPHEPHEBC233233
21111TRPTRPVALVALAA238 - 240238 - 240
22111TRPTRPVALVALBC238 - 240238 - 240
23121PROPROSERSERAA245 - 250245 - 250
24121PROPROSERSERBC245 - 250245 - 250
25131PHEPHETRPTRPAA254 - 255254 - 255
26131PHEPHETRPTRPBC254 - 255254 - 255
27141F3SF3SSF4SF4AF - G266 - 267
28141F3SF3SSF4SF4BU - V266 - 267
112ILEILEGLYGLYHB17 - 1917 - 19
212ILEILEGLYGLYID17 - 1917 - 19
322ARGARGARGARGHB4343
422ARGARGARGARGID4343
532GLUGLUGLUGLUHB4646
632GLUGLUGLUGLUID4646
742THRTHRALAALAHB61 - 7361 - 73
842THRTHRALAALAID61 - 7361 - 73
952ALAALAALAALAHB7575
1052ALAALAALAALAID7575
1162METMETMETMETHB100100
1262METMETMETMETID100100
1372GLNGLNGLNGLNHB103103
1472GLNGLNGLNGLNID103103
1582ASPASPHISHISHB107 - 108107 - 108
1682ASPASPHISHISID107 - 108107 - 108
1792LEULEULEULEUHB115115
1892LEULEULEULEUID115115
19102LYSLYSLYSLYSHB216216
20102LYSLYSLYSLYSID216216
21112HISHISHISHISHB219219
22112HISHISHISHISID219219
23122GLNGLNGLNGLNHB221221
24122GLNGLNGLNGLNID221221
25132GLUGLUGLUGLUHB321321
26132GLUGLUGLUGLUID321321
27142TYRTYRTYRTYRHB328328
28142TYRTYRTYRTYRID328328
29152THRTHRTHRTHRHB341341
30152THRTHRTHRTHRID341341
31162METMETLYSLYSHB357 - 358357 - 358
32162METMETLYSLYSID357 - 358357 - 358
33172VALVALVALVALHB369369
34172VALVALVALVALID369369
35182VALVALHISHISHB459 - 468459 - 468
36182VALVALHISHISID459 - 468459 - 468
37192PHEPHETHRTHRHB480 - 487480 - 487
38192PHEPHETHRTHRID480 - 487480 - 487
39202ASNASNLEULEUHB489 - 490489 - 490
40202ASNASNLEULEUID489 - 490489 - 490
41212TYRTYRHISHISHB527 - 536527 - 536
42212TYRTYRHISHISID527 - 536527 - 536
43222FCOFCOMGMGHO - N537 - 540
44222FCOFCOMGMGIAA - Z537 - 540

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a heterodimer, two copies of which are in the asymmetric unit

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Components

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Periplasmic [NiFe] hydrogenase ... , 2 types, 4 molecules ABHI

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


Mass: 28351.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P12943, cytochrome-c3 hydrogenase
#2: Protein Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 59657.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / Cellular location: periplasm / Strain: wild type / References: UniProt: P12944, cytochrome-c3 hydrogenase

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Non-polymers , 9 types, 540 molecules

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


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


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2S
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#10: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / pH: 6.3
Details: PEG8000, sodium chloride, N,N-dimethyl dodecylamine N-oxide, glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 26, 1996
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→19.8 Å / Num. obs: 58639 / % possible obs: 86.2 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 37.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 8.4
Reflection shellResolution: 2.35→2.45 Å / % possible all: 78.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.501data extraction
ProDCdata collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FRV
Resolution: 2.35→13 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.217 / Stereochemistry target values: ENGH & HUBER / Details: USE OF TLS PARAMETERS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2962 5.1 %RANDOM
Rwork0.132 ---
obs0.135 58485 92.2 %-
all-61447 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å2-1.11 Å20.02 Å2
2--0.13 Å20.9 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.35→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12237 0 114 515 12866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.94417258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39751577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33724.079554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.933152013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1891563
X-RAY DIFFRACTIONr_chiral_restr0.0820.21877
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029663
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.25868
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.28549
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2659
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1571.58071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.473212638
X-RAY DIFFRACTIONr_scbond_it1.96925333
X-RAY DIFFRACTIONr_scangle_it2.5234566
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
1A326tight positional0.060.2
2H505tight positional0.090.2
1A326tight thermal0.341
2H505tight thermal0.411
LS refinement shellResolution: 2.35→2.45 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.203 321 -
Rwork0.134 5612 -
obs--78.23 %
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)
10.6345-0.1110.37240.7022-0.35181.73330.0486-0.0474-0.1371-0.07090.02390.1170.1584-0.0708-0.07250.0579-0.0057-0.03570.0582-0.01220.127419.02676.82548.693
20.4494-0.14310.13390.6852-0.25971.3222-0.0127-0.02680.05860.0635-0.00270.01-0.33290.08710.01550.1245-0.0206-0.00660.0785-0.02290.101225.72599.59751.667
31.04860.0221-0.07241.987-0.71471.336-0.1617-0.1416-0.11320.39730.2130.2827-0.1676-0.1965-0.05130.09310.10330.05890.14690.00850.1372-13.33259.43925.144
41.033-0.0973-0.09141.7898-0.64041.2001-0.1557-0.0943-0.33050.12130.0586-0.16020.1690.1460.09710.07510.06920.04130.1153-0.00440.23262.90942.07421.917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 264
2X-RAY DIFFRACTION1A265 - 267
3X-RAY DIFFRACTION1A264
4X-RAY DIFFRACTION1A1268 - 1273
5X-RAY DIFFRACTION2H7 - 536
6X-RAY DIFFRACTION2H537 - 540
7X-RAY DIFFRACTION2H1541 - 1544
8X-RAY DIFFRACTION3B5 - 264
9X-RAY DIFFRACTION3B265 - 267
10X-RAY DIFFRACTION3B2268
11X-RAY DIFFRACTION4I7 - 536
12X-RAY DIFFRACTION4I537 - 540
13X-RAY DIFFRACTION4I2541

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  • 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

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