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- PDB-3wyo: Heterodimeric myoglobin formed by domain swapping -

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Basic information

Entry
Database: PDB / ID: 3wyo
TitleHeterodimeric myoglobin formed by domain swapping
Components(Myoglobin) x 2
KeywordsOXYGEN BINDING / Globin
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Helix Hairpins - #2100 / Helix Hairpins - #2110 / Helix Hairpins / Myoglobin / Globin family profile. / Globin / Globin / Helix non-globular / Globin-like superfamily / Special
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, Y.W. / Nagao, S. / Zhang, M. / Shomura, Y. / Higuchi, Y. / Hirota, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Rational design of heterodimeric protein using domain swapping for myoglobin.
Authors: Lin, Y.W. / Nagao, S. / Zhang, M. / Shomura, Y. / Higuchi, Y. / Hirota, S.
History
DepositionSep 4, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
C: Myoglobin
D: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4008
Polymers67,9344
Non-polymers2,4664
Water6,395355
1
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2004
Polymers33,9672
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-90 kcal/mol
Surface area14890 Å2
MethodPISA
2
C: Myoglobin
D: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2004
Polymers33,9672
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-87 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.702, 72.168, 161.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 1 - 153 / Label seq-ID: 1 - 153

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Myoglobin /


Mass: 16997.672 Da / Num. of mol.: 2 / Mutation: H64V/V68H/E85K/D141K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Protein Myoglobin /


Mass: 16969.355 Da / Num. of mol.: 2 / Mutation: K78E/K79D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 1000, 100mM MES-NaOH buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 49418 / Num. obs: 45097 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 27
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2198 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WLA
Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.215 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26616 2004 4.9 %RANDOM
Rwork0.22595 ---
obs0.22795 39225 91.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-0 Å20 Å2
2--0.23 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 172 355 5323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195136
X-RAY DIFFRACTIONr_bond_other_d0.0070.024976
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9996964
X-RAY DIFFRACTIONr_angle_other_deg1.364311491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2775614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69725.116215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55415921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.291158
X-RAY DIFFRACTIONr_chiral_restr0.1220.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025772
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021174
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_it0.7381.0782459
X-RAY DIFFRACTIONr_mcbond_other0.7371.0772458
X-RAY DIFFRACTIONr_mcangle_it1.2231.613072
X-RAY DIFFRACTIONr_mcangle_other1.2231.6113073
X-RAY DIFFRACTIONr_scbond_it0.9731.3072677
X-RAY DIFFRACTIONr_scbond_other0.9681.3062675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5621.9233892
X-RAY DIFFRACTIONr_long_range_B_refined5.85710.2666438
X-RAY DIFFRACTIONr_long_range_B_other5.7569.7756270
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A81320.11
12B81320.11
21A82570.13
22C82570.13
31A81320.11
32D81320.11
41B78840.13
42C78840.13
51B81850.12
52D81850.12
61C80660.12
62D80660.12
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 97 -
Rwork0.262 1583 -
obs--51.47 %
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)
11.1963-0.36540.43612.5781-0.72955.07470.0675-0.0736-0.14290.123-0.0122-0.06040.59170.1427-0.05540.21940.014-0.00120.11460.0110.20734.2581-7.3532-38.981
21.5617-0.9991-0.47535.8112.53156.62620.03690.15340.0653-0.2655-0.0993-0.07190.14250.13030.06250.1580.02840.02680.18650.01920.15038.34740.7485-55.3469
33.29340.167-1.4661.59991.081112.80770.01280.04750.0206-0.03170.0234-0.18590.17850.1423-0.03630.16490.05840.00130.14660.01570.211.9529-3.4917-37.9334
43.5196-1.5972-0.4784.87862.951818.12290.17-0.22030.2519-0.0366-0.3016-0.0427-0.2750.39320.13170.252-0.0026-0.00770.1620.04790.190611.5478-3.7628-20.7613
51.95770.829-0.02554.06772.74895.63730.1508-0.08510.02410.3887-0.54850.25850.8456-1.24890.39770.1944-0.12510.07190.4076-0.04120.06785.87240.7161-2.1406
633.90461.6623-0.71830.6641-1.860520.47570.57860.75882.4255-0.00950.45540.257-2.01460.2403-1.03410.4235-0.17870.03590.5160.04180.338215.400921.1817-1.5022
73.37194.52152.082123.06252.44316.8441-0.11660.06230.475-0.01110.24970.3712-0.5591-0.2927-0.13310.16180.12260.02590.29040.01960.2067.79416.5345-9.9996
83.90655.28880.4422.92533.34274.67810.195-0.2063-0.1630.4081-0.64851.14320.6242-0.86270.45350.1724-0.1130.01030.4669-0.08960.1481.3719-2.8175-10.2668
90.2709-0.12841.54446.17551.349613.17340.10020.12890.0176-0.03370.0099-0.21570.24430.1299-0.11020.16450.0406-0.01040.21530.00250.205311.601615.1318-19.3257
102.28621.7656-2.4092.6367-2.29987.90820.0622-0.12860.24380.15140.0630.0582-0.36630.0841-0.12520.20140.0717-0.02110.2368-0.02280.180817.194111.9996-1.8876
113.286-0.42743.15581.5552-3.27168.5308-0.2062-0.5673-0.0688-0.32170.1685-0.05740.6136-0.84920.03770.4773-0.07940.05940.3654-0.00730.00878.120.795611.2031
120.05230.05880.50070.438-0.445214.5064-0.0318-0.0503-0.02250.1553-0.064-0.0676-0.0890.20720.09580.19550.0633-0.00210.265-0.0030.161617.59874.04943.9239
132.41490.17884.02692.3036-1.690313.42140.1533-0.2068-0.190.0279-0.0307-0.04670.71060.3737-0.12260.22870.05030.00880.16440.01740.166414.73916.012-22.6529
141.27331.31710.09473.26520.06831.85530.02710.00570.04940.0343-0.12180.1338-0.00180.04020.09470.18850.02810.0070.13860.00690.19133.61251.9299-40.713
151.94834.20510.615411.41840.50940.79720.2031-0.12240.02880.5514-0.2240.18610.1072-0.14210.02090.2036-0.00650.02290.153-0.00350.18330.9689-0.8144-31.4058
1613.6165-9.94734.611614.7743-12.208911.9714-0.881-0.1578-0.241.1311.04020.2233-0.8934-1.1647-0.15920.30870.0691-0.02920.156-0.1020.3695.639218.5817-32.0486
177.6783-1.65887.0385.8696-2.719315.96860.15630.42190.7082-0.5671-0.2267-0.35690.07960.45810.07040.16030.01890.09050.2062-0.03080.2344-17.563511.3515-23.0839
186.12052.2965-2.84354.9965-1.29994.3502-0.2488-0.5425-0.10750.21320.101-0.38590.13330.45120.14780.12190.1461-0.04770.3058-0.00370.1457-21.47561.9417-5.5943
192.5913.77432.965.57684.093411.0209-0.2217-0.3943-0.2597-0.3343-0.4338-0.37870.3376-0.08840.65560.29920.14580.00670.41250.11140.1924-23.3052-7.49011.5254
201.5550.0449-0.09993.0995-5.14720.9387-0.0968-0.2242-0.18070.0410.0776-0.18540.16040.43420.01930.1320.05860.00570.2582-0.02620.3074-14.62790.2349-16.2888
216.87640.91071.12214.64580.127911.29770.1288-0.07760.8190.0321-0.37860.0358-0.6471-0.31010.24980.17550.08330.07470.149-0.04240.2665-16.574613.0554-47.4298
223.039-2.1305-0.73310.12562.00092.27470.11410.055-0.07560.0997-0.06760.4540.2931-0.425-0.04650.11780.0199-0.01570.2504-0.02940.1982-23.6723-5.7674-53.6541
231.6077-0.1052-0.710313.04491.69192.58090.1607-0.1562-0.01730.2687-0.14430.540.0847-0.3137-0.01640.09580.02370.02790.2604-0.01820.2718-24.8867-0.5286-42.9702
2430.763-13.40718.427610.1589-11.957718.42870.14730.5953-0.6982-0.00980.34570.5811-0.4431-0.9988-0.49290.6982-0.0235-0.31910.1369-0.0670.4943-24.17216.5898-42.3522
2514.53762.6926-9.1544.64132.919813.2752-0.1131-1.1115-0.34680.92220.03570.37130.56190.27880.07740.43160.22560.19530.3910.16480.3103-21.8709-11.7626-36.7415
261.2431-1.8802-0.17745.388-2.17994.43580.14580.0643-0.0119-0.2865-0.14050.05730.211-0.1592-0.00530.16230.019-0.02020.1793-0.0380.2216-16.3492-6.6658-54.4349
273.83320.20490.30654.9844-5.09065.2934-0.23370.25070.24770.11690.0023-0.2079-0.262-0.0280.23140.50580.25980.05530.17230.05540.1637-17.4099.9177-62.8637
282.2910.0696-1.16581.8196-2.219112.41980.0750.37380.1149-0.3199-0.21410.05350.04980.05850.13910.20310.05690.01090.2007-0.01570.2282-12.2099-0.2208-58.1088
2914.1891-2.7059-1.106512.9062-0.327319.70520.04-0.11540.06340.30630.01720.2529-0.35920.1286-0.05720.2145-0.01070.04450.1636-0.04670.1802-15.9133-5.4036-33.2973
304.9201-2.0096-3.084.74724.4266.8055-0.50710.0006-0.61680.3225-0.03410.10841.0020.16290.54120.23780.07510.12050.13950.04940.1589-24.6223-10.2796-16.828
312.13580.1726-1.12944.16970.57441.9083-0.0161-0.08330.1762-0.2843-0.0255-0.1353-0.1893-0.06770.04160.12750.0449-0.00270.2211-0.01880.2176-24.82035.9499-17.5047
3229.20391.2278-5.48592.28634.382224.38080.2091-0.46230.12330.01260.08710.8325-0.2603-0.8237-0.29620.29990.02710.06570.10910.19880.5945-30.1469-15.2653-23.6353
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 39
2X-RAY DIFFRACTION2A40 - 63
3X-RAY DIFFRACTION3A64 - 77
4X-RAY DIFFRACTION4A78 - 86
5X-RAY DIFFRACTION5A87 - 114
6X-RAY DIFFRACTION6A115 - 122
7X-RAY DIFFRACTION7A123 - 136
8X-RAY DIFFRACTION8A137 - 153
9X-RAY DIFFRACTION9B1 - 8
10X-RAY DIFFRACTION10B9 - 32
11X-RAY DIFFRACTION11B33 - 51
12X-RAY DIFFRACTION12B52 - 76
13X-RAY DIFFRACTION13B77 - 87
14X-RAY DIFFRACTION14B88 - 120
15X-RAY DIFFRACTION15B121 - 147
16X-RAY DIFFRACTION16B148 - 153
17X-RAY DIFFRACTION17C1 - 16
18X-RAY DIFFRACTION18C17 - 39
19X-RAY DIFFRACTION19C40 - 55
20X-RAY DIFFRACTION20C56 - 86
21X-RAY DIFFRACTION21C87 - 100
22X-RAY DIFFRACTION22C101 - 124
23X-RAY DIFFRACTION23C125 - 147
24X-RAY DIFFRACTION24C148 - 153
25X-RAY DIFFRACTION25D1 - 8
26X-RAY DIFFRACTION26D9 - 36
27X-RAY DIFFRACTION27D37 - 49
28X-RAY DIFFRACTION28D50 - 77
29X-RAY DIFFRACTION29D78 - 84
30X-RAY DIFFRACTION30D85 - 106
31X-RAY DIFFRACTION31D107 - 146
32X-RAY DIFFRACTION32D147 - 153

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