[English] 日本語
Yorodumi
- PDB-5hhl: Reverse transcriptase domain of group II intron maturase from Eub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hhl
TitleReverse transcriptase domain of group II intron maturase from Eubacterium rectale in P21 space group
ComponentsRetron-type reverse transcriptase
KeywordsRNA BINDING PROTEIN / Group II intron
Function / homology
Function and homology information


RNA-directed DNA polymerase activity
Similarity search - Function
Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / Retron-type reverse transcriptase
Similarity search - Component
Biological speciesEubacterium rectale M104/1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhao, C. / Pyle, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM50313 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution.
Authors: Zhao, C. / Pyle, A.M.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retron-type reverse transcriptase
B: Retron-type reverse transcriptase
C: Retron-type reverse transcriptase
D: Retron-type reverse transcriptase
E: Retron-type reverse transcriptase
F: Retron-type reverse transcriptase
G: Retron-type reverse transcriptase
H: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,04916
Polymers265,7378
Non-polymers3138
Water22,5191250
1
A: Retron-type reverse transcriptase
B: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5124
Polymers66,4342
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-7 kcal/mol
Surface area25480 Å2
MethodPISA
2
C: Retron-type reverse transcriptase
H: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5124
Polymers66,4342
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-7 kcal/mol
Surface area25010 Å2
MethodPISA
3
D: Retron-type reverse transcriptase
E: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5124
Polymers66,4342
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-7 kcal/mol
Surface area25230 Å2
MethodPISA
4
F: Retron-type reverse transcriptase
G: Retron-type reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5124
Polymers66,4342
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-8 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.830, 119.860, 161.470
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Retron-type reverse transcriptase


Mass: 33217.070 Da / Num. of mol.: 8 / Fragment: UNP residues 1-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale M104/1 (bacteria) / Gene: ERE_01490 / Production host: Escherichia coli (E. coli) / References: UniProt: D4JMT6
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1250 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES/imidazole pH 6.5, 20 mM sodium formate, 20 mM NH4OAc, 20 mM trisodium citrate, 20 mM sodium potassium L-tartrate, 20 mM sodium oxamate, 10 % PEG 8000, 20 % EG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→49.143 Å / Num. obs: 165153 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 8.12

-
Processing

Software
NameVersionClassification
PHENIX(dev_2254: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HHJ
Resolution: 2.1→49.143 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 8256 5 %
Rwork0.2008 --
obs0.2027 165139 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18416 0 8 1250 19674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00118819
X-RAY DIFFRACTIONf_angle_d0.42425357
X-RAY DIFFRACTIONf_dihedral_angle_d11.97411611
X-RAY DIFFRACTIONf_chiral_restr0.0412782
X-RAY DIFFRACTIONf_plane_restr0.0033330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.34492460.31364728X-RAY DIFFRACTION91
2.1239-2.14890.32692770.29685250X-RAY DIFFRACTION100
2.1489-2.17510.31982730.2935225X-RAY DIFFRACTION100
2.1751-2.20260.33322760.28145224X-RAY DIFFRACTION100
2.2026-2.23160.32292750.26965214X-RAY DIFFRACTION100
2.2316-2.26220.31822740.26015249X-RAY DIFFRACTION100
2.2622-2.29450.27442730.24885168X-RAY DIFFRACTION100
2.2945-2.32870.26852780.24435280X-RAY DIFFRACTION100
2.3287-2.36510.32542730.2495205X-RAY DIFFRACTION100
2.3651-2.40390.29032790.24635280X-RAY DIFFRACTION100
2.4039-2.44530.26862740.2315214X-RAY DIFFRACTION100
2.4453-2.48980.27182800.23125249X-RAY DIFFRACTION100
2.4898-2.53770.2842720.23225207X-RAY DIFFRACTION100
2.5377-2.58950.28362780.22775267X-RAY DIFFRACTION100
2.5895-2.64580.28862710.23525205X-RAY DIFFRACTION100
2.6458-2.70730.26892790.22135234X-RAY DIFFRACTION100
2.7073-2.7750.27332790.22225297X-RAY DIFFRACTION100
2.775-2.85010.24772730.21055190X-RAY DIFFRACTION100
2.8501-2.93390.28582720.22245254X-RAY DIFFRACTION100
2.9339-3.02860.25992800.225243X-RAY DIFFRACTION100
3.0286-3.13680.25632770.22265276X-RAY DIFFRACTION100
3.1368-3.26240.28472760.21715234X-RAY DIFFRACTION100
3.2624-3.41080.22882760.2055243X-RAY DIFFRACTION100
3.4108-3.59060.23662770.19145252X-RAY DIFFRACTION100
3.5906-3.81550.21742760.18095255X-RAY DIFFRACTION100
3.8155-4.110.20482770.1695270X-RAY DIFFRACTION100
4.11-4.52330.18912750.15375253X-RAY DIFFRACTION100
4.5233-5.17720.16632810.14755298X-RAY DIFFRACTION100
5.1772-6.52030.20712780.17655287X-RAY DIFFRACTION100
6.5203-49.15670.19042810.17265332X-RAY DIFFRACTION99
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)
10.4684-0.4348-0.04170.601-0.16090.2026-0.0792-0.00180.3036-0.2129-0.0707-0.1612-0.2997-0.0215-00.4318-0.0367-0.01390.48840.040.382246.293599.684877.1048
20.2358-0.08870.06110.33030.14160.1056-0.049-0.03620.002-0.0665-0.1827-0.21710.27830.1349-00.3318-0.04270.01420.51220.04440.415851.962188.204789.6972
30.26280.2457-0.22131.1924-0.18640.6224-0.04070.0281-0.0571-0.0977-0.0226-0.13620.06940.037700.2655-0.03590.01160.40320.02480.324139.403777.842981.0303
40.46970.3429-0.25890.3077-0.39480.8907-0.0688-0.0741-0.1749-0.2210.05-0.34090.31290.15450.05190.22050.03430.0830.3012-0.03880.460640.457857.892983.3898
50.31360.1105-0.03010.2255-0.16820.13590.1048-0.1351-0.1160.1487-0.1085-0.0537-0.07430.1182-0.00210.1796-0.03290.0240.27020.03240.315431.332467.763995.4107
60.3299-0.1595-0.18880.33180.060.1761-0.03170.1886-0.282-0.3850.0570.37390.36490.0428-0.0070.4174-0.0894-0.06270.55070.03730.5211.292868.518583.4926
70.0705-0.1295-0.08690.27560.21960.2104-0.053-0.1307-0.07070.10990.2570.32750.10390.00180.00590.2635-0.0140.01160.57630.07780.4262.589275.99799.3808
80.50770.25130.20960.69620.11450.7286-0.03110.08680.0497-0.07190.02740.238-0.0977-0.15810.01110.2475-0.0308-0.0310.41710.03590.362410.661489.514289.7084
90.12560.1261-0.01180.21850.08830.1036-0.1546-0.07280.35370.14620.06240.0873-0.3245-0.22200.33960.0315-0.0150.39390.01220.369814.8378102.5977100.183
100.0482-0.05970.06210.0752-0.07730.0815-0.2258-0.1059-0.2710.120.1167-0.0581-0.1181-0.2065-0.01620.2072-0.09370.01680.25160.03490.271835.206892.493999.9591
110.0586-0.0780.1590.1366-0.2820.5863-0.2184-0.37780.10090.45020.046-0.0711-0.20370.0964-0.27210.78240.0685-0.07370.4642-0.1080.295129.837788.3599173.7189
120.61060.12920.65550.02730.1390.7035-0.4489-0.44940.52390.4017-0.030.0552-0.609-0.3774-0.77280.83370.1818-0.1580.3846-0.11620.430323.240697.6751166.7928
131.23850.91540.24190.68510.18510.1663-0.52010.01530.09580.09340.16340.3871-0.3249-0.2149-0.41720.56630.14440.0560.3824-0.07690.31418.056286.7596155.4941
140.3336-0.19130.44170.7153-0.37191.0801-0.1106-0.1240.020.15370.0921-0.0033-0.0888-0.1852-00.42720.01730.0460.279-0.01430.240625.989271.2181161.4442
150.209-0.23510.08990.2897-0.05890.1039-0.1065-0.0569-0.0522-0.03620.12190.25550.1447-0.3190.00060.3648-0.08080.05750.2704-0.00840.247821.020158.0576151.4799
160.052-0.01840.00930.05010.0330.0309-0.13250.18830.30490.09890.2037-0.00820.0344-0.08980.00010.4085-0.01610.040.294-0.01180.340841.48362.0825141.7275
170.83660.2259-0.70681.10530.07930.6793-0.10870.5890.0844-0.20930.1035-0.0352-0.2472-0.2487-0.23830.32090.0237-0.08280.25320.05410.438216.873122.7482115.8877
180.9409-0.20390.27620.7492-0.00090.6854-0.05880.03520.05930.09270.01210.1166-0.0766-0.0383-0.01520.1813-0.0408-0.00220.1169-0.0150.239728.4018113.621135.8673
190.2386-0.11020.01060.32070.00120.00010.0811-0.11440.19130.2666-0.1433-0.1373-0.53640.36810.00440.4187-0.1737-0.03330.3292-0.07530.432362.7731119.9497136.9909
200.84490.7788-0.11021.97530.86790.76570.065-0.1654-0.01620.6005-0.1319-0.37640.05610.2842-0.60490.2967-0.1427-0.1230.3264-0.01160.398568.1439108.4439142.0676
210.0471-0.08120.12820.3176-0.07620.4683-0.0561-0.20210.0425-0.1152-0.0856-0.03840.15380.17130.00550.2616-0.0719-0.03690.4519-0.06980.540664.0989100.193128.441
220.3128-0.04320.3580.8406-0.14490.5271-0.07510.2226-0.0117-0.0487-0.0101-0.0815-0.19390.1902-00.2948-0.0946-0.02010.3593-0.03690.310256.7178114.2248119.56
230.0588-0.03250.02010.0174-0.01560.04020.0867-0.1452-0.02410.18410.0369-0.02480.14610.05620.00010.3213-0.0155-0.01190.403-0.06250.368853.6135103.8111126.0639
240.1332-0.1027-0.03690.07840.02850.00970.05640.17940.2286-0.3087-0.10770.1016-0.07450.0541-00.3308-0.0733-0.02150.33290.0110.269551.4788114.5745110.9605
250.0408-0.0416-0.03320.04230.03380.0266-0.00750.11440.0124-0.514-0.0618-0.1671-0.38790.155700.4636-0.00480.05730.5824-0.01650.317652.2424109.931698.6239
260.1135-0.1428-0.06240.20010.08460.0771-0.05980.0013-0.2429-0.02210.06670.04120.2331-0.01310.00010.24690.0026-0.03180.49-0.08320.285649.194102.9212107.3776
270.0440.0244-0.02170.0151-0.00210.06290.0194-0.4107-0.1880.139-0.0999-0.05290.00320.0504-00.3457-0.056-0.03880.5312-0.06280.374830.2575103.5797113.6277
280.94430.4083-0.10820.1776-0.04760.0186-0.29610.4003-0.13580.13820.24510.00240.2763-0.1018-0.05850.70010.02790.01170.4799-0.11410.36839.63531.378697.8007
291.34690.80310.10811.0040.27810.0948-0.21510.69540.0439-0.96820.2051-0.0945-0.11610.0475-0.09570.7321-0.04030.07510.5514-0.07080.336545.335740.948190.5733
300.16790.1388-0.11870.118-0.1180.1798-0.04020.3592-0.2383-0.0446-0.1145-0.10830.21990.57440.00220.55830.0250.02970.4377-0.04580.460351.511246.7971102.1501
310.27650.20660.25530.17430.2120.25330.03480.1802-0.1349-0.0283-0.04320.05540.2186-0.019300.47950.01320.02080.2952-0.04920.313637.453237.1312115.2173
320.06280.03910.02120.1160.08330.06030.25730.25060.05960.1806-0.0079-0.0997-0.1960.167-00.48790.02590.04020.5308-0.06620.33946.935145.2982126.5698
330.08890.00190.02560.01020.01760.03440.16090.2873-0.05180.07090.1012-0.15680.25360.47170.0020.56550.2267-0.03480.5576-0.12260.49654.396930.3939109.1904
340.02990.03140.03190.03380.03420.0341-0.0004-0.03740.1464-0.06130.1073-0.09280.09540.0607-00.4692-0.00440.00620.4658-0.03030.360741.495748.1842110.7499
350.07640.01260.05330.029-0.00020.03930.10890.0304-0.22550.1153-0.10360.00180.10980.231400.50260.0444-0.01040.3144-0.03550.320343.662137.6693125.9157
360.03180.02810.02480.02490.02020.02480.15680.0641-0.08060.4046-0.075-0.36060.26760.140.00010.56140.0355-0.05610.484-0.02570.394651.33841.4915136.1589
370.11780.09550.01220.08840.030.03380.00270.12230.03840.10270.1707-0.1144-0.10770.1421-0.00010.4108-0.03520.02410.3837-0.06350.329246.563649.2579129.0593
380.0177-0.0204-0.00220.08790.02870.01490.01570.15880.16490.0178-0.0892-0.1104-0.042-0.124-0.00010.4346-0.04250.0430.3168-0.03280.297727.519254.34132.3464
391.21480.32560.02631.4699-0.27960.05820.3379-0.5922-0.13360.6443-0.20050.10080.384-0.5340.19590.8202-0.31040.09250.51230.06420.417610.930936.2845140.4819
400.41470.0072-0.03160.1623-0.16040.1652-0.0572-0.1253-0.02150.1059-0.07820.1320.3421-0.2888-0.75880.4323-0.20580.18160.5056-0.02150.42017.818252.2801133.4527
410.67120.04430.19340.51440.17161.18910.10180-0.01410.166-0.13260.12990.1896-0.29540.08890.2341-0.09310.0710.2437-0.01360.259212.594846.8052114.1654
420.61210.48720.47450.39450.29872.74640.0806-0.0106-0.36490.76260.2291-0.71810.7349-0.0799-0.23270.69050.1104-0.27520.45040.06660.521860.400553.5766152.7013
430.4882-0.0550.04180.0390.0790.3461-0.019-0.16570.00520.65460.0147-0.75340.16290.1716-0.01380.42930.0271-0.22030.27350.04340.536957.385674.0257155.2794
440.2982-0.1014-0.19550.31690.01610.13360.03540.16630.03790.0667-0.0298-0.4228-0.09540.15810.00990.309-0.0747-0.04430.26050.02440.547551.591288.9184147.372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 234 )
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 251 )
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 292 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 56 )
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 234 )
9X-RAY DIFFRACTION9chain 'B' and (resid 235 through 274 )
10X-RAY DIFFRACTION10chain 'B' and (resid 275 through 292 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 26 )
12X-RAY DIFFRACTION12chain 'C' and (resid 27 through 56 )
13X-RAY DIFFRACTION13chain 'C' and (resid 57 through 84 )
14X-RAY DIFFRACTION14chain 'C' and (resid 85 through 234 )
15X-RAY DIFFRACTION15chain 'C' and (resid 235 through 274 )
16X-RAY DIFFRACTION16chain 'C' and (resid 275 through 291 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 84 )
18X-RAY DIFFRACTION18chain 'D' and (resid 85 through 292 )
19X-RAY DIFFRACTION19chain 'E' and (resid 3 through 26 )
20X-RAY DIFFRACTION20chain 'E' and (resid 27 through 56 )
21X-RAY DIFFRACTION21chain 'E' and (resid 57 through 84 )
22X-RAY DIFFRACTION22chain 'E' and (resid 85 through 177 )
23X-RAY DIFFRACTION23chain 'E' and (resid 178 through 198 )
24X-RAY DIFFRACTION24chain 'E' and (resid 199 through 234 )
25X-RAY DIFFRACTION25chain 'E' and (resid 235 through 251 )
26X-RAY DIFFRACTION26chain 'E' and (resid 252 through 274 )
27X-RAY DIFFRACTION27chain 'E' and (resid 275 through 291 )
28X-RAY DIFFRACTION28chain 'F' and (resid 4 through 26 )
29X-RAY DIFFRACTION29chain 'F' and (resid 27 through 56 )
30X-RAY DIFFRACTION30chain 'F' and (resid 57 through 84 )
31X-RAY DIFFRACTION31chain 'F' and (resid 85 through 131 )
32X-RAY DIFFRACTION32chain 'F' and (resid 132 through 150 )
33X-RAY DIFFRACTION33chain 'F' and (resid 151 through 177 )
34X-RAY DIFFRACTION34chain 'F' and (resid 178 through 198 )
35X-RAY DIFFRACTION35chain 'F' and (resid 199 through 234 )
36X-RAY DIFFRACTION36chain 'F' and (resid 235 through 251 )
37X-RAY DIFFRACTION37chain 'F' and (resid 252 through 274 )
38X-RAY DIFFRACTION38chain 'F' and (resid 275 through 291 )
39X-RAY DIFFRACTION39chain 'G' and (resid 4 through 56 )
40X-RAY DIFFRACTION40chain 'G' and (resid 57 through 84 )
41X-RAY DIFFRACTION41chain 'G' and (resid 85 through 292 )
42X-RAY DIFFRACTION42chain 'H' and (resid 2 through 84 )
43X-RAY DIFFRACTION43chain 'H' and (resid 85 through 234 )
44X-RAY DIFFRACTION44chain 'H' and (resid 235 through 291 )

+
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