[English] 日本語
Yorodumi
- PDB-6fxq: Structure of coproheme decarboxylase from Listeria monocytogenes ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fxq
TitleStructure of coproheme decarboxylase from Listeria monocytogenes during turnover
ComponentsPutative heme-dependent peroxidase lmo2113
KeywordsOXIDOREDUCTASE / coproheme decarboxylase / iron coproporphyrin III / monovinyl monopropionate deuteroheme
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / heme biosynthetic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Apc35880; domain 1 / Coproheme decarboxylase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FEC / harderoheme (III) / Coproheme decarboxylase
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHofbauer, S. / Pfanzagl, V. / Mlynek, G. / Puehringer, D.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29099 Austria
CitationJournal: Acs Catalysis / Year: 2019
Title: Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Hemeb.
Authors: Milazzo, L. / Gabler, T. / Puhringer, D. / Jandova, Z. / Maresch, D. / Michlits, H. / Pfanzagl, V. / Djinovic-Carugo, K. / Oostenbrink, C. / Furtmuller, P.G. / Obinger, C. / Smulevich, G. / Hofbauer, S.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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_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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative heme-dependent peroxidase lmo2113
B: Putative heme-dependent peroxidase lmo2113
C: Putative heme-dependent peroxidase lmo2113
D: Putative heme-dependent peroxidase lmo2113
E: Putative heme-dependent peroxidase lmo2113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,20124
Polymers143,7585
Non-polymers7,44319
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23830 Å2
ΔGint-246 kcal/mol
Surface area45740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.687, 129.369, 77.916
Angle α, β, γ (deg.)90.000, 105.520, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Putative heme-dependent peroxidase lmo2113 / UPF0447 protein lmo2113


Mass: 28751.527 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2113 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8Y5F1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

-
Non-polymers , 5 types, 730 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FEC / 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX / FE-COPROPORPHYRIN III


Mass: 708.538 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C36H36FeN4O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-VOV / harderoheme (III)


Mass: 662.513 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C35H34FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M bicine pH 9.0 10 % (w/v) PEG6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.69→49.004 Å / Num. obs: 162948 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 26.81 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.131 / Rrim(I) all: 0.231 / Net I/σ(I): 2.93
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 1.748 / Rpim(I) all: 1.223 / Rrim(I) all: 2.141

-
Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_2645refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WWS

4wws


Resolution: 1.69→49.004 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2144 1976 1.22 %
Rwork0.1784 --
obs0.1789 161811 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 228.97 Å2 / Biso mean: 43.1452 Å2 / Biso min: 15.97 Å2
Refinement stepCycle: final / Resolution: 1.69→49.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9801 0 883 711 11395
Biso mean--62.13 42.1 -
Num. residues----1203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410613
X-RAY DIFFRACTIONf_angle_d1.23814479
X-RAY DIFFRACTIONf_chiral_restr0.0651428
X-RAY DIFFRACTIONf_plane_restr0.0081823
X-RAY DIFFRACTIONf_dihedral_angle_d15.1666154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6901-1.73240.41521300.3988104521058290
1.7324-1.77920.3841390.3782112621140197
1.7792-1.83160.36881400.3559112801142097
1.8316-1.89070.36011380.3192113731151197
1.8907-1.95830.31061480.2701114881163699
1.9583-2.03670.28751390.225114821162199
2.0367-2.12940.2231410.1984115501169199
2.1294-2.24170.18681450.1796115621170799
2.2417-2.38210.21961430.1619114381158198
2.3821-2.5660.20511420.1581116121175499
2.566-2.82420.20121420.1593115761171899
2.8242-3.23280.2121420.1582115921173499
3.2328-4.07270.19391420.1384115411168398
4.0727-49.02490.16131450.1521116271177298
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)
10.5920.1616-0.4210.1652-0.10580.28120.1255-0.1371-0.0508-0.0028-0.1719-0.00340.31020.22310.01870.3103-0.0358-0.00960.2887-0.0060.2119-24.46078.7998105.6849
20.34330.2588-0.12840.2076-0.0460.0920.0544-0.2573-0.0867-0.08760.11580.22840.3191-0.7520.00010.3238-0.12270.01060.46280.03840.3794-36.1088-0.32103.5116
30.49750.26250.17060.4005-0.01380.05860.2233-0.47040.0728-0.0421-0.11260.33810.1228-0.29-0.06580.2647-0.07030.00540.34150.01050.2494-27.34728.2696110.6587
40.00420-0.02540.08010.02030.12640.1907-0.3287-0.0328-0.0858-0.0248-0.04010.31210.0119-0.00020.3526-0.064-0.02120.28230.03010.2941-22.266-1.8363104.6143
50.0515-0.0547-0.06920.0550.06770.07940.0616-0.2775-0.21870.0078-0.0017-0.02810.0517-0.12100.2819-0.068-0.01070.2755-0.02180.2453-22.56968.8674102.1758
60.18950.04980.07230.14410.01310.13310.1407-0.49390.12690.3476-0.0071-0.0093-0.17590.5614-0.00010.522-0.0570.05570.66990.01280.376-16.69593.9249132.6627
70.1560.0851-0.07540.03650.0370.14550.0612-0.31950.05010.1403-0.03730.0630.1415-0.09080.00050.291-0.04070.02710.4325-0.02250.2374-24.200914.4952118.1733
80.1304-0.1531-0.00010.13620.00250.01840.14160.14750.06130.00620.1521-0.0457-0.26840.5132-0.00030.3117-0.04920.01590.4307-0.02650.2428-0.655821.7946122.5613
90.2156-0.2870.05281.3271-0.10630.03570.0701-0.32310.02540.52-0.1632-0.00780.4286-0.1333-0.07420.4156-0.10240.03370.5889-0.04550.1979-12.975920.9209132.3013
100.32760.39560.25440.5030.3320.68070.1024-0.4390.06220.1103-0.07370.02090.0986-0.19580.07320.2644-0.04350.02680.441-0.04370.2114-20.967919.424120.1048
110.22160.1321-0.2380.0035-0.0490.4928-0.0235-0.28140.05470.04650.0170.0076-0.0374-0.2345-00.2382-0.03240.00910.4326-0.00820.2553-25.916118.602111.7311
120.95370.0357-0.11980.4828-0.24760.1414-0.1531-0.21980.06930.1806-0.07930.07810.2957-0.1945-00.2339-0.00430.01010.3074-0.05750.2887-29.956329.383695.2103
130.3453-0.28640.01230.18940.01710.02940.02830.08250.05540.0006-0.03380.05980.2457-0.0862-0.00010.2441-0.014-0.00240.3818-0.04540.3383-42.749230.212189.9816
140.30610.18740.30640.08710.11330.3084-0.0108-0.14120.2096-0.0135-0.0520.0967-0.0168-0.1879-0.00410.22720.02460.00260.2898-0.04160.3718-32.101334.74898.2022
150.05130.04930.00190.13860.0430.0739-0.0519-0.3738-0.0168-0.0556-0.14770.19040.3604-0.4248-0.00030.29850.0010.020.4413-0.01680.3755-37.203423.1622100.9347
160.2559-0.0669-0.13470.0972-0.01320.09520.0589-0.3015-0.01050.0222-0.07980.05120.0602-0.36470.00020.24550.0053-0.00890.3148-0.06060.2842-27.977426.169295.7701
170.0169-0.02090.00380.0211-0.00080.0189-0.1852-0.0112-0.21140.38360.05360.1732-0.2510.3684-0.00010.5525-0.00360.08090.6036-0.21570.6155-35.162642.244117.2913
180.28490.03260.36320.3951-0.23790.54580.0836-0.38430.2250.0575-0.06710.02010.0227-0.1105-0.00310.25470.00180.00020.3417-0.11240.332-18.78838.9145110.52
190.0565-0.06490.03520.2870.1670.28560.0312-0.13030.23630.0902-0.13160.11970.0183-0.4053-0.25210.32860.09280.10860.3275-0.58660.3466-17.043148.9666118.6579
200.4054-0.193-0.01150.37080.31640.3380.0145-0.19170.19490.0543-0.04990.0663-0.0683-0.0642-0.0030.25290.0279-0.00670.2779-0.10910.347-20.767343.2499105.4116
210.32640.2266-0.29860.6694-0.03680.329-0.0469-0.05550.2116-0.0515-0.01170.1608-0.1154-0.00810.00010.21810.0488-0.00070.2486-0.07020.3614-22.722339.283896.7637
220.3461-0.1062-0.37480.76090.16180.32340.09650.0351-0.11080.0166-0.0741-0.1670.23190.1088-0.00040.33490.0049-0.0160.22350.0160.2662-3.92182.025496.0763
230.6268-0.0014-0.16310.1943-0.32420.49090.10360.1378-0.50490.1407-0.00470.22340.2121-0.1762-0.01650.43420.0101-0.0680.162-0.01840.355-8.1206-11.884388.89
240.3450.17080.30.1815-0.05980.5266-0.0086-0.0754-0.19830.0901-0.0183-0.01080.15640.1123-00.31250.0291-0.00220.23090.03070.2826-2.8903-3.137798.756
250.2648-0.09870.1710.11050.00490.2567-0.0110.6473-0.0379-0.1767-0.0037-0.14620.2520.35140.0030.3830.0073-0.00920.27510.00790.28370.8498-1.340686.5527
260.1192-0.0516-0.11650.09990.13550.1519-0.0951-0.01440.0535-0.08340.1022-0.01010.0721-0.027800.3236-0.0132-0.01020.1914-0.01350.2518-6.42323.948392.8504
270.526-0.0404-0.20070.16090.29880.7744-0.0539-0.5827-0.40330.0476-0.116-0.15120.11260.8077-0.05170.53090.0918-0.05570.49140.17890.402811.4862-4.4768107.3909
280.1878-0.0477-0.07490.132-0.0320.40440.2131-0.4691-0.01130.1509-0.24440.01810.00370.13990.00010.2852-0.0292-0.01550.36930.00520.24016.616415.2502111.1422
290.04-0.08440.05360.1557-0.08220.06190.3076-0.0753-0.34410.0261-0.1377-0.27240.21070.44140.00040.38250.0026-0.08350.68420.05120.417713.87838.8844120.5475
300.3617-0.01710.18050.4590.34170.66010.0892-0.3042-0.0260.1125-0.1222-0.05780.05140.1478-00.2820.0062-0.02770.31880.03650.22690.76716.1017112.702
310.0094-0.0020.02270.00380.00680.03440.17530.0635-0.2740.21570.10520.07240.5155-0.243-0.00010.53530.0167-0.04480.340.12020.4602-16.2758-10.02798.2564
320.94960.1552-0.03840.23570.04160.8799-0.01650.08930.03-0.04780.0541-0.03240.03310.1481-00.2630.00420.00490.2409-0.00770.21344.590915.945776.3857
330.06180.00620.00250.0767-0.08310.0996-0.07550.2450.3254-0.1029-0.0010.3279-0.1947-0.049-0.00010.29220.0166-0.01180.2898-0.00310.26990.303523.986271.7981
340.0809-0.1035-0.12960.19080.09470.2304-0.0491-0.1169-0.0859-0.0368-0.01040.0252-0.0760.0501-00.2423-0.0035-0.00620.2497-0.00650.2343-1.8718.098480.7476
350.2107-0.07860.10980.1945-0.05320.0653-0.0409-0.27110.78320.1572-0.0158-0.2024-0.22590.43250.00020.3833-0.0444-0.00370.61890.02210.509325.980832.598482.8514
360.6759-0.02310.00560.0096-0.03770.0078-0.0562-0.12780.0632-0.01340.05610.0020.08060.166-00.25530.01670.00510.2914-0.02330.260513.133125.33394.424
370.2522-0.02720.14110.1162-0.00610.0511-0.09690.04960.251-0.08810.1608-0.2641-0.0680.35650.00010.2782-0.01020.0110.4694-0.0340.412824.63827.778399.5111
380.25580.05870.23180.13990.19610.3930.01240.0630.2062-0.02820.0545-0.2542-0.02690.1871-00.2420.01110.00670.2951-0.00760.27913.676121.780289.383
390.2911-0.1060.14220.16860.22230.32160.1173-0.19130.0604-0.0552-0.0443-0.07740.00450.117800.25510.0117-0.00650.3534-0.00730.272315.483418.7887101.2816
400.2351-0.0020.03450.08230.0203-0.0062-0.030.1504-0.14890.12960.2424-0.15730.19890.402-0.00010.27340.02240.03150.2717-0.01930.27095.42495.101879.96
410.5798-0.27030.20490.3136-0.30870.25790.03610.00660.19-0.2337-0.0061-0.1818-0.3254-0.10350.01250.24130.0108-0.01560.1628-0.00010.2664-13.501933.92279.7586
420.0110.08450.0470.2639-0.16740.3382-0.04770.29980.2907-0.6055-0.03730.1343-0.12160.02420.00050.3895-0.0087-0.08460.26310.06680.3155-18.831437.091567.3595
430.20250.14930.24690.13990.23550.39260.0039-0.01350.3085-0.4291-0.0239-0.0521-0.1483-0.0403-00.2680.0173-0.03370.18080.03250.3498-10.507139.591978.7233
440.07350.0405-0.0810.116-0.0330.0626-0.0380.2380.0326-0.0612-0.1270.309-0.0036-0.33060.00010.29190.0423-0.01510.27620.00850.3564-23.224938.991280.4804
450.7429-0.2795-0.3970.1558-0.03820.61530.09690.00450.37540.1003-0.08270.0026-0.1953-0.0085-0.0110.28220.0082-0.02820.16050.01220.4008-9.777646.384284.1851
460.18240.12260.07050.06750.02890.1120.0178-0.20510.111-0.03130.03890.0159-0.05530.17630.00010.2555-0.0067-0.01280.3029-0.06730.333-1.103142.0784100.7238
470.6185-0.1618-0.22730.17-0.1470.4398-0.0353-0.53280.3914-0.2143-0.06590.2024-0.56010.15430.00690.4348-0.0446-0.05040.3756-0.08040.62876.162353.042698.5024
480.4457-0.05040.29080.23470.04820.23370.0161-0.15090.3163-0.0381-0.02510.0478-0.1360.0895-0.00030.2832-0.02290.00440.1843-0.01220.3539-3.23244.115588.6446
490.252-0.02430.1920.17960.00470.11110.06110.02570.3928-0.05720.0821-0.088-0.1920.12960.00010.2838-0.0214-0.00460.2583-0.02920.39947.344340.737294.149
500.1432-0.0627-0.09050.19270.0780.0731-0.07270.13120.16690.0036-0.0212-0.0536-0.02990.5379-0.00310.29380.02420.01280.23150.03830.2733-5.228432.581971.392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 29 )A4 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 52 )A30 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 78 )A53 - 78
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 92 )A79 - 92
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 107 )A93 - 107
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 134 )A108 - 134
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 151 )A135 - 151
8X-RAY DIFFRACTION8chain 'A' and (resid 152 through 163 )A152 - 163
9X-RAY DIFFRACTION9chain 'A' and (resid 164 through 181 )A164 - 181
10X-RAY DIFFRACTION10chain 'A' and (resid 182 through 221 )A182 - 221
11X-RAY DIFFRACTION11chain 'A' and (resid 222 through 251 )A222 - 251
12X-RAY DIFFRACTION12chain 'B' and (resid 6 through 29 )B6 - 29
13X-RAY DIFFRACTION13chain 'B' and (resid 30 through 52 )B30 - 52
14X-RAY DIFFRACTION14chain 'B' and (resid 53 through 78 )B53 - 78
15X-RAY DIFFRACTION15chain 'B' and (resid 79 through 92 )B79 - 92
16X-RAY DIFFRACTION16chain 'B' and (resid 93 through 107 )B93 - 107
17X-RAY DIFFRACTION17chain 'B' and (resid 108 through 134 )B108 - 134
18X-RAY DIFFRACTION18chain 'B' and (resid 135 through 163 )B135 - 163
19X-RAY DIFFRACTION19chain 'B' and (resid 164 through 181 )B164 - 181
20X-RAY DIFFRACTION20chain 'B' and (resid 182 through 221 )B182 - 221
21X-RAY DIFFRACTION21chain 'B' and (resid 222 through 251 )B222 - 251
22X-RAY DIFFRACTION22chain 'C' and (resid 3 through 29 )C3 - 29
23X-RAY DIFFRACTION23chain 'C' and (resid 30 through 52 )C30 - 52
24X-RAY DIFFRACTION24chain 'C' and (resid 53 through 78 )C53 - 78
25X-RAY DIFFRACTION25chain 'C' and (resid 79 through 92 )C79 - 92
26X-RAY DIFFRACTION26chain 'C' and (resid 93 through 107 )C93 - 107
27X-RAY DIFFRACTION27chain 'C' and (resid 108 through 142 )C108 - 142
28X-RAY DIFFRACTION28chain 'C' and (resid 143 through 163 )C143 - 163
29X-RAY DIFFRACTION29chain 'C' and (resid 164 through 180 )C164 - 180
30X-RAY DIFFRACTION30chain 'C' and (resid 181 through 239 )C181 - 239
31X-RAY DIFFRACTION31chain 'C' and (resid 240 through 251 )C240 - 251
32X-RAY DIFFRACTION32chain 'D' and (resid 2 through 78 )D2 - 78
33X-RAY DIFFRACTION33chain 'D' and (resid 79 through 92 )D79 - 92
34X-RAY DIFFRACTION34chain 'D' and (resid 93 through 107 )D93 - 107
35X-RAY DIFFRACTION35chain 'D' and (resid 108 through 134 )D108 - 134
36X-RAY DIFFRACTION36chain 'D' and (resid 135 through 163 )D135 - 163
37X-RAY DIFFRACTION37chain 'D' and (resid 164 through 181 )D164 - 181
38X-RAY DIFFRACTION38chain 'D' and (resid 182 through 208 )D182 - 208
39X-RAY DIFFRACTION39chain 'D' and (resid 209 through 233 )D209 - 233
40X-RAY DIFFRACTION40chain 'D' and (resid 234 through 251 )D234 - 251
41X-RAY DIFFRACTION41chain 'E' and (resid 6 through 29 )E6 - 29
42X-RAY DIFFRACTION42chain 'E' and (resid 30 through 52 )E30 - 52
43X-RAY DIFFRACTION43chain 'E' and (resid 53 through 78 )E53 - 78
44X-RAY DIFFRACTION44chain 'E' and (resid 79 through 92 )E79 - 92
45X-RAY DIFFRACTION45chain 'E' and (resid 93 through 142 )E93 - 142
46X-RAY DIFFRACTION46chain 'E' and (resid 143 through 163 )E143 - 163
47X-RAY DIFFRACTION47chain 'E' and (resid 164 through 181 )E164 - 181
48X-RAY DIFFRACTION48chain 'E' and (resid 182 through 208 )E182 - 208
49X-RAY DIFFRACTION49chain 'E' and (resid 209 through 233 )E209 - 233
50X-RAY DIFFRACTION50chain 'E' and (resid 234 through 251 )E234 - 251

+
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