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- PDB-3ze8: 3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenb... -

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Basic information

Entry
Database: PDB / ID: 3ze8
Title3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the reduced state at 1.95 Angstroms
Components(PERIPLASMIC [NIFESE] HYDROGENASE, ...) x 2
KeywordsOXIDOREDUCTASE / HYDROGENASE BIOHYDROGEN OXYGEN TOLERANCE
Function / homology
Function and homology information


ferredoxin hydrogenase / 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 ...ferredoxin hydrogenase / 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 ...: / 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
Chem-C15 / CARBONMONOXIDE-(DICYANO) IRON / : / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsMarques, M.C. / Coelho, R. / Pereira, I.A.C. / Matias, P.M.
Citation
Journal: Int.J.Hydrogen Energy / Year: 2013
Title: Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough
Authors: Marques, M.C. / Coelho, R. / Pereira, I.A.C. / Matias, P.M.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: The Three-Dimensional Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough: A Hydrogenase without a Bridging Ligand in the Active Site in its Oxidised, "as-Isolated" State.
Authors: Marques, M.C. / Coelho, R. / De Lacey, A.L. / Pereira, I.A.C. / Matias, P.M.
History
DepositionDec 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _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_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Polymer sequence
Category: entity_poly / exptl_crystal_grow ...entity_poly / exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.method ..._entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 3.2Jun 3, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_sheet_hbond.range_1_auth_atom_id ..._pdbx_database_status.status_code_sf / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 3.3Dec 20, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
B: PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,71614
Polymers83,6932
Non-polymers3,02412
Water11,512639
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-101.7 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.227, 97.632, 103.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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PERIPLASMIC [NIFESE] HYDROGENASE, ... , 2 types, 2 molecules AB

#1: Protein PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT


Mass: 30261.568 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-317 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING


Mass: 53431.121 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-495 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 7 types, 651 molecules

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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H38NO3S
#5: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSIGNAL PEPTIDE CLEAVED OFF MATURE PROTEIN

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CRYSTALS WERE GROWN USING THE SITTING-DROP VAPOR DIFFUSION METHOD AT 20C BY MIXING 1.5 UL OF RESERVOIR SOLUTION CONTAINING 20% POLYETHYLENE GLYCOL (PEG) 1500, 0.1 M TRIS-HCL, PH 8.5 AND AN ...Details: CRYSTALS WERE GROWN USING THE SITTING-DROP VAPOR DIFFUSION METHOD AT 20C BY MIXING 1.5 UL OF RESERVOIR SOLUTION CONTAINING 20% POLYETHYLENE GLYCOL (PEG) 1500, 0.1 M TRIS-HCL, PH 8.5 AND AN EQUAL VOLUME OF A SOLUTION COMPOSED OF 10 MG/ML OF PROTEIN IN 10 MM TRIS-HCL BUFFER AT PH 7.6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→44.1 Å / Num. obs: 64222 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.1 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPN

2wpn


Resolution: 1.801→44.14 Å / SU ML: 0.14 / σ(F): 1.24 / Phase error: 14.89 / Stereochemistry target values: ML
Details: REFINEMENT PROTOCOL USED SEPARATE FRIEDEL PAIRS. TOTAL NUMBER OF NON-ANOMALOUS REFLECTIONS 64168
RfactorNum. reflection% reflection
Rfree0.1658 5953 5.1 %
Rwork0.1352 --
obs0.1368 64166 90.15 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 83 639 6547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086170
X-RAY DIFFRACTIONf_angle_d1.1048345
X-RAY DIFFRACTIONf_dihedral_angle_d13.8272320
X-RAY DIFFRACTIONf_chiral_restr0.074907
X-RAY DIFFRACTIONf_plane_restr0.0051078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.82140.24431820.20023668X-RAY DIFFRACTION90
1.8214-1.84280.18812060.18453920X-RAY DIFFRACTION93
1.8428-1.86530.23642290.1773741X-RAY DIFFRACTION93
1.8653-1.88890.20992320.16993839X-RAY DIFFRACTION93
1.8889-1.91380.21042140.17143832X-RAY DIFFRACTION93
1.9138-1.940.20272040.16573745X-RAY DIFFRACTION91
1.94-1.96770.16891900.14813909X-RAY DIFFRACTION93
1.9677-1.99710.20112420.15113738X-RAY DIFFRACTION92
1.9971-2.02830.17981660.14073854X-RAY DIFFRACTION93
2.0283-2.06160.17262130.13823776X-RAY DIFFRACTION91
2.0616-2.09710.16971910.14113796X-RAY DIFFRACTION92
2.0971-2.13520.1951770.13713809X-RAY DIFFRACTION92
2.1352-2.17630.15141920.13163804X-RAY DIFFRACTION91
2.1763-2.22070.18092070.13023795X-RAY DIFFRACTION92
2.2207-2.2690.17622180.14443687X-RAY DIFFRACTION91
2.269-2.32180.16591950.13263762X-RAY DIFFRACTION91
2.3218-2.37980.16632120.13493810X-RAY DIFFRACTION91
2.3798-2.44420.16892040.12663692X-RAY DIFFRACTION90
2.4442-2.51610.15811860.12873750X-RAY DIFFRACTION91
2.5161-2.59730.17241930.12333730X-RAY DIFFRACTION90
2.5973-2.69010.17841820.13223737X-RAY DIFFRACTION90
2.6901-2.79780.18512060.12923694X-RAY DIFFRACTION89
2.7978-2.92510.18011790.13383663X-RAY DIFFRACTION89
2.9251-3.07930.15921820.1353686X-RAY DIFFRACTION88
3.0793-3.27220.15091900.13273638X-RAY DIFFRACTION88
3.2722-3.52470.13812180.12823592X-RAY DIFFRACTION87
3.5247-3.87920.12882090.12023580X-RAY DIFFRACTION87
3.8792-4.44010.11731680.10713588X-RAY DIFFRACTION86
4.4401-5.59230.13882170.11763489X-RAY DIFFRACTION85
5.5923-44.15290.18441490.14263471X-RAY DIFFRACTION83
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)
11.7978-0.49640.22211.4223-0.39010.4025-0.0166-0.29870.0550.28060.057-0.0078-0.0391-0.0025-0.0410.1504-0.00570.00650.1427-0.0130.0807-16.1211-24.01737.0186
21.40040.57990.51381.2711-0.18370.9506-0.0141-0.1289-0.0190.1570.0439-0.0712-0.04990.0729-0.03160.1110.0298-0.00210.1165-0.00850.1005-5.0181-29.252533.8116
31.1037-0.20570.08180.7768-0.05690.4401-0.0269-0.1621-0.08790.13690.0322-0.05170.00410.0257-0.0090.1249-0.0005-0.00640.10650.01250.095-16.9433-36.064236.4826
40.9098-0.0226-0.060.91070.05680.5509-0.0021-0.1496-0.0790.18290.01130.1060.0352-0.055-0.00510.1221-0.01120.03760.10960.00680.1027-38.0323-30.118136.3248
53.92040.7916-4.4522.77441.17556.702-0.1166-0.3855-0.112-0.104-0.01190.02280.06090.11090.1310.1408-0.00350.0520.1567-0.00340.1871-45.9977-29.300634.8799
65.04714.46651.93353.98421.91672.08620.1376-0.11510.2394-0.0864-0.143-0.01530.1489-0.0713-0.010.1465-0.00460.02070.1572-0.00440.1492-34.6134-27.590133.9758
73.665-0.59963.04614.6298-4.71846.46250.0005-0.02480.07620.06210.0826-0.20460.1250.1067-0.07120.12670.01420.01810.13560.00840.1315-22.957-28.841628.7182
81.70860.7565-0.30121.9533-0.38841.3233-0.13560.0806-0.1833-0.09370.0671-0.26850.10950.16940.0890.08380.00060.01160.101-0.02680.10511.3057-21.852518.4184
95.65962.9356-1.22872.5414-0.99210.4785-0.10240.1767-0.2701-0.09140.0659-0.10120.01460.01060.04380.0787-0.0030.01020.0706-0.04120.0494-12.3829-28.121314.0014
100.72070.19570.13580.410.04990.30450.013-0.07210.07570.0788-0.00880.0281-0.0422-0.0283-0.00410.10030.00680.01390.0763-0.01760.0752-23.7369-12.232427.4084
110.50270.0779-0.0020.4553-0.00030.2898-0.01130.05980.0394-0.03150.01320.0038-0.0076-0.0043-0.0020.0697-0.00090.0030.0715-0.00710.052-17.1468-13.112511.7732
124.06664.3195-3.76654.5968-3.9983.4895-0.1388-0.2979-0.77640.17270.13020.26390.4533-0.05780.02450.11180.01630.0280.1593-0.02680.1628-19.8569-18.802718.7781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:32)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 33:97)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 98:181)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 182:283)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 284)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 285)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 286)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 15:40)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 41:60)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 61:220)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 221:495)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 500:501)

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  • 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

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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

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