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- PDB-4a25: X-ray structure Dps from Kineococcus radiotolerans in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4a25
TitleX-ray structure Dps from Kineococcus radiotolerans in complex with Mn (II) ions.
ComponentsFERRITIN DPS FAMILY PROTEIN
KeywordsMETAL BINDING PROTEIN / DETOXIFICATION PROCESS
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis
Similarity search - Function
Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin Dps family protein
Similarity search - Component
Biological speciesKINEOCOCCUS RADIOTOLERANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIlari, A. / Fiorillo, A. / Ardini, M. / Stefanini, S. / Chiancone, E.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Kineococcus Radiotolerans Dps Forms a Heteronuclear Mn-Fe Ferroxidase Center that May Explain the Mn-Dependent Protection Against Oxidative Stress.
Authors: Ardini, M. / Fiorillo, A. / Fittipaldi, M. / Stefanini, S. / Gatteschi, D. / Llari, A. / Chiancone, E.
History
DepositionSep 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: 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_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_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_seq_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.ptnr3_symmetry / _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.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_label_seq_id / _struct_conn.ptnr2_symmetry / _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: FERRITIN DPS FAMILY PROTEIN
B: FERRITIN DPS FAMILY PROTEIN
C: FERRITIN DPS FAMILY PROTEIN
D: FERRITIN DPS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,84120
Polymers74,0794
Non-polymers76216
Water5,495305
1
A: FERRITIN DPS FAMILY PROTEIN
B: FERRITIN DPS FAMILY PROTEIN
C: FERRITIN DPS FAMILY PROTEIN
D: FERRITIN DPS FAMILY PROTEIN
hetero molecules

A: FERRITIN DPS FAMILY PROTEIN
B: FERRITIN DPS FAMILY PROTEIN
C: FERRITIN DPS FAMILY PROTEIN
D: FERRITIN DPS FAMILY PROTEIN
hetero molecules

A: FERRITIN DPS FAMILY PROTEIN
B: FERRITIN DPS FAMILY PROTEIN
C: FERRITIN DPS FAMILY PROTEIN
D: FERRITIN DPS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,52260
Polymers222,23612
Non-polymers2,28648
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area60350 Å2
ΔGint-379.8 kcal/mol
Surface area60680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.474, 150.474, 86.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1172-

MN

21A-1174-

CL

31D-1170-

MN

41D-1171-

MN

51A-2030-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 168
2114B2 - 168
3114C2 - 168
4114D2 - 168

NCS oper:
IDCodeMatrixVector
1given(-0.36418, 0.66985, 0.64705), (0.66341, -0.30103, 0.68503), (0.65365, 0.67873, -0.33476)18.79828, 20.00192, -38.93121
2given(0.75932, -0.01426, 0.65056), (-0.59199, -0.43018, 0.68153), (0.27014, -0.90263, -0.33509)18.93197, 19.85516, -38.78126
3given(0.13825, 0.95357, 0.26756), (0.3774, 0.19905, -0.9044), (-0.91567, 0.22602, -0.33236)7.85285, -26.32122, -38.74152

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Components

#1: Protein
FERRITIN DPS FAMILY PROTEIN / DPS


Mass: 18519.654 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KINEOCOCCUS RADIOTOLERANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6WG04
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.36 % / Description: NONE
Crystal growpH: 8
Details: MPD (2-METHYL-2,4-PENTANEDIOL) 45 %, TRIS-HCL 0.1 M, PH 8.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49300 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 16.7 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 40.94
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 7.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z90
Resolution: 2→75.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.849 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23226 2491 5.1 %RANDOM
Rwork0.1942 ---
obs0.19608 46797 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å20 Å2
2---0.74 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2→75.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5149 0 16 305 5470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9397193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.865679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30323.75264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76715860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.351558
X-RAY DIFFRACTIONr_chiral_restr0.0840.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214056
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_it0.3861.53349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59525403
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16731924
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8144.51784
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

Ens-ID: 1 / Number: 1234 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.220.5
2Bmedium positional0.210.5
3Cmedium positional0.190.5
4Dmedium positional0.260.5
1Amedium thermal0.752
2Bmedium thermal0.572
3Cmedium thermal0.612
4Dmedium thermal0.642
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 203 -
Rwork0.239 3411 -
obs--99.18 %
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)
115.00823.6579-0.647320.19274.92781.37320.5938-1.3793-0.05871.2236-0.4879-0.29290.254-0.0187-0.1060.2981-0.05750.03190.56040.10630.3224-35.4059-16.3626-7.011
23.14420.7178-1.76445.9269-3.33652.4922-0.0809-0.0304-0.08930.14130.32260.5177-0.0166-0.1998-0.24180.1859-0.04720.02020.34710.01010.4062-39.6673-11.5911-16.3435
34.6732-0.9183-3.70734.65875.54379.217-0.05770.07350.1370.0534-0.13790.5835-0.0809-0.60510.19560.19340.03040.0030.24690.08260.2737-37.34-9.2039-40.5344
41.77750.0034-0.80261.04960.0781.2133-0.03290.2794-0.0805-0.26370.04130.15560.0626-0.0761-0.00850.1091-0.0064-0.07150.1088-0.01660.054-17.5706-11.5574-48.5352
53.2387-2.0226-0.33921.55740.54550.4508-0.00370.0797-0.1755-0.16690.02130.0992-0.09210.0496-0.01770.3782-0.0323-0.06360.2932-0.03850.069-11.4279-12.9018-62.8055
67.0654-1.6007-4.52291.0170.81623.61550.15690.38670.158-0.3124-0.05220.225-0.209-0.1963-0.10470.212-0.0007-0.11490.2347-0.0130.1412-26.1705-3.4516-54.1328
76.48421.1127-5.27861.6233-0.9655.78250.02680.17340.0888-0.17110.020.1575-0.04090.0169-0.04680.13950.0114-0.10170.14510.01740.0878-22.22471.3371-48.0542
80.69112.3748-0.6458.1957-1.99575.6390.08720.01760.22090.347-0.00170.7239-0.5347-0.6719-0.08550.28390.0045-0.01950.29010.00170.2229-13.12197.6812-66.0162
90.19330.1966-0.350115.82672.818415.1301-0.10810.4225-0.3099-1.2080.4571-0.73920.85040.6833-0.3490.4253-0.08560.10591.1505-0.63930.791515.8896-4.1725-70.9166
105.60134.6348-2.78027.5286-5.27063.7706-0.5260.7098-0.1642-1.11520.1911-0.41910.8145-0.05340.33490.6117-0.01650.02740.5642-0.09370.388715.9298-12.3064-67.8943
113.28940.7312-0.73251.85341.86092.5896-0.25551.00130.8625-0.69110.46540.1893-0.6720.092-0.20990.5459-0.0603-0.0660.54710.07790.42998.1009-24.5051-61.5915
121.7731-0.1915-0.99751.06240.33372.4163-0.00040.2342-0.236-0.2380.01890.08780.1149-0.0266-0.01850.1158-0.0226-0.06490.06-0.03660.11-12.7963-22.0239-43.0131
138.4453-2.7774-1.14354.3205-0.03242.19930.00040.2452-0.2873-0.1255-0.08830.20170.2466-0.43470.08790.1052-0.0633-0.06760.0924-0.01080.2366-25.4357-27.515-36.0725
145.4973-1.6709-4.71252.18150.97994.6115-0.17380.0915-0.4471-0.1610.02380.03960.31150.05750.150.145-0.0312-0.05720.0996-0.07560.2008-10.6229-33.3029-39.2388
153.26030.2692-3.55861.2858-0.27595.87130.03920.0977-0.1478-0.19350.0398-0.08720.06270.1489-0.07910.0969-0.0077-0.05280.0571-0.03620.1451-3.0759-28.7959-37.1093
163.5313-1.9263-1.92532.44261.33591.1125-0.04630.246-0.0871-0.1499-0.00140.07780.0221-0.11220.04770.2825-0.0551-0.00460.12850.030.2531-12.0878-40.0303-17.9737
1711.2069-1.20471.9770.5109-0.60270.8245-0.1546-0.27531.15870.31410.0014-0.1324-0.5001-0.06380.15320.6707-0.01320.04570.22130.00910.2903-15.431142.4893-31.9256
180.14670.70710.23154.3741.26770.4081-0.0136-0.08320.18710.3236-0.1780.6519-0.012-0.1080.19150.34230.03450.03660.3387-0.04060.5239-25.421632.3548-33.3202
191.5326-1.28370.12773.7279-0.46651.05170.0329-0.0675-0.05680.05560.01020.3606-0.0019-0.1656-0.04320.0258-0.02340.04350.10050.00220.1179-26.4234-1.2168-17.1008
201.75080.41631.11045.0533-2.84514.03480.01390.05660.12-0.0573-0.0219-0.0293-0.006-0.00180.0080.01190.0090.02860.0888-0.00580.0858-24.48511.1851-23.9322
211.13570.267-0.02063.9864-1.03561.9082-0.0104-0.0748-0.03670.1270.04830.48220.0496-0.3519-0.03790.05820.02380.07610.1453-0.02240.2063-32.65927.8146-12.2442
222.5573-0.00152.67991.6513-0.69918.30330.0572-0.1176-0.25060.1504-0.0034-0.05370.32230.0417-0.05370.1112-0.01220.02830.14330.00870.1794-30.2626-12.8481-12.7452
230.9735-0.41140.02293.7794-0.98571.01550.01960.07880.0175-0.07520.00850.3264-0.0481-0.1594-0.02810.0373-0.0098-0.01930.1239-0.00350.1741-32.67620.9919-28.659
245.7463-1.47242.54412.65892.82837.6403-0.0319-0.02130.033-0.0729-0.0890.23650.0389-0.33610.12090.126-0.0433-0.02780.18790.01220.3332-36.8159-22.6284-30.6815
256.3725-4.02125.892313.52887.44121.3798-0.0356-0.6597-0.80330.68730.04980.69730.8511-0.6113-0.01430.3269-0.0060.02730.33830.0810.3953-15.1936-35.2342-5.5177
264.23340.77121.64155.3451-0.0883.53910.2416-0.2569-0.29990.4786-0.17660.28450.282-0.0868-0.06510.3789-0.01370.03470.35450.07940.2668-13.2548-27.6811.2867
275.2111-4.8559-0.12734.58180.09750.0448-0.0587-0.0193-0.42970.02850.01130.27150.14210.00940.04740.51940.01490.02170.33750.02940.3312-16.0101-7.78078.2109
281.40530.2413-0.31343.4274-2.27862.64210.0197-0.15870.09630.20970.00250.1724-0.0598-0.034-0.02220.05670.00870.0430.0766-0.04480.0686-17.332213.7339-11.6658
290.7714-0.28630.03511.3996-0.24340.451-0.0255-0.25820.05590.2660.02520.1756-0.0386-0.09120.00030.12210.0040.07480.1489-0.02330.0731-19.31279.5584-4.1542
304.1502-2.112-2.09063.2031.58992.5295-0.1578-0.530.19990.64930.1814-0.08370.0605-0.0203-0.02360.32010.01420.01860.27570.00150.0616-9.1438-0.41538.0553
310.8673-0.0153-0.05156.357-1.11670.5910.0126-0.06750.02040.0583-0.0357-0.0659-0.00250.03470.02310.12150.00110.00680.1424-0.02020.105-6.659313.0888-4.5679
326.4863.11153.17993.51420.87692.30910.0618-0.6646-0.39920.5152-0.0971-0.353-0.0106-0.09120.03530.3680.0732-0.0110.3573-0.01590.3278-4.33729.7882-3.0799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 5
2X-RAY DIFFRACTION2A6 - 19
3X-RAY DIFFRACTION3A20 - 31
4X-RAY DIFFRACTION4A32 - 99
5X-RAY DIFFRACTION5A100 - 111
6X-RAY DIFFRACTION6A112 - 137
7X-RAY DIFFRACTION7A138 - 163
8X-RAY DIFFRACTION8A164 - 168
9X-RAY DIFFRACTION9B2 - 6
10X-RAY DIFFRACTION10B7 - 14
11X-RAY DIFFRACTION11B15 - 24
12X-RAY DIFFRACTION12B25 - 98
13X-RAY DIFFRACTION13B99 - 111
14X-RAY DIFFRACTION14B112 - 134
15X-RAY DIFFRACTION15B135 - 164
16X-RAY DIFFRACTION16B165 - 170
17X-RAY DIFFRACTION17C2 - 9
18X-RAY DIFFRACTION18C10 - 21
19X-RAY DIFFRACTION19C22 - 67
20X-RAY DIFFRACTION20C68 - 84
21X-RAY DIFFRACTION21C85 - 105
22X-RAY DIFFRACTION22C106 - 119
23X-RAY DIFFRACTION23C120 - 164
24X-RAY DIFFRACTION24C165 - 170
25X-RAY DIFFRACTION25D3 - 7
26X-RAY DIFFRACTION26D8 - 19
27X-RAY DIFFRACTION27D20 - 27
28X-RAY DIFFRACTION28D28 - 70
29X-RAY DIFFRACTION29D71 - 129
30X-RAY DIFFRACTION30D130 - 144
31X-RAY DIFFRACTION31D145 - 163
32X-RAY DIFFRACTION32D164 - 168

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