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- PDB-5n1p: Crystal structure of the polysaccharide deacetylase Bc1974 from B... -

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Basic information

Entry
Database: PDB / ID: 5n1p
TitleCrystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with N-hydroxynaphthalene-1-carboxamide
ComponentsPeptidoglycan N-acetylglucosamine deacetylase
KeywordsHYDROLASE / CE4 domain / polysaccharide deacetylase / PgdA / Bacillus cereus
Function / homology
Function and homology information


peptidoglycan-N-acetylglucosamine deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function
: / : / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
~{N}-oxidanylnaphthalene-1-carboxamide / TRIETHYLENE GLYCOL / Peptidoglycan-N-acetylglucosamine deacetylase BC_1974
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.448 Å
AuthorsGiastas, P. / Andreou, A. / Eliopoulos, E.E.
Funding support Greece, 1items
OrganizationGrant numberCountry
GSRT GreeceSyn 11-3-1321 Greece
CitationJournal: Biochemistry / Year: 2018
Title: Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors.
Authors: Giastas, P. / Andreou, A. / Papakyriakou, A. / Koutsioulis, D. / Balomenou, S. / Tzartos, S.J. / Bouriotis, V. / Eliopoulos, E.E.
History
DepositionFeb 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Experimental preparation / Source and taxonomy / Category: entity_src_gen / exptl_crystal_grow
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _exptl_crystal_grow.temp
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan N-acetylglucosamine deacetylase
B: Peptidoglycan N-acetylglucosamine deacetylase
C: Peptidoglycan N-acetylglucosamine deacetylase
D: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,89916
Polymers93,6304
Non-polymers1,26912
Water11,205622
1
A: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6603
Polymers23,4081
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7224
Polymers23,4081
Non-polymers3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6834
Polymers23,4081
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8335
Polymers23,4081
Non-polymers4264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)196.103, 44.347, 99.132
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Peptidoglycan N-acetylglucosamine deacetylase


Mass: 23407.607 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC_1974 / Production host: Escherichia coli (E. coli)
References: UniProt: Q81EJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 634 molecules

#2: Chemical
ChemComp-8GK / ~{N}-oxidanylnaphthalene-1-carboxamide


Mass: 187.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C11H9NO2 / Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-ZN / ZINC ION / Peptidoglycan-N-acetylglucosamine deacetylase / Polysaccharide deacetylase


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: AT268_30040, B4155_0776, TQ94_03800, TU58_19865, WR51_09920, WR52_09510
Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM sodium citrate pH 5.6, 10% ethanol, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.448→48.445 Å / Num. obs: 149666 / % possible obs: 98.93 % / Redundancy: 5.1 % / Net I/σ(I): 1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.448→48.445 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.1798 14542 5.01 %
Rwork0.1613 --
obs0.1622 149666 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.448→48.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 16 622 7290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066907
X-RAY DIFFRACTIONf_angle_d1.0999334
X-RAY DIFFRACTIONf_dihedral_angle_d12.0012538
X-RAY DIFFRACTIONf_chiral_restr0.042963
X-RAY DIFFRACTIONf_plane_restr0.0061215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4483-1.46480.39554020.39227632X-RAY DIFFRACTION82
1.4648-1.4820.32924930.33119264X-RAY DIFFRACTION99
1.482-1.50010.32394810.31869129X-RAY DIFFRACTION100
1.5001-1.51910.32144910.3019259X-RAY DIFFRACTION100
1.5191-1.53910.32484880.30819312X-RAY DIFFRACTION100
1.5391-1.56020.32834860.31429240X-RAY DIFFRACTION100
1.5602-1.58250.32124850.29439287X-RAY DIFFRACTION100
1.5825-1.60610.27194840.27999256X-RAY DIFFRACTION100
1.6061-1.63120.26484890.24679230X-RAY DIFFRACTION100
1.6312-1.65790.24084910.2289325X-RAY DIFFRACTION100
1.6579-1.68650.22134880.21199212X-RAY DIFFRACTION100
1.6865-1.71720.21464930.18969338X-RAY DIFFRACTION100
1.7172-1.75020.20724920.18019307X-RAY DIFFRACTION100
1.7502-1.78590.21444970.18019324X-RAY DIFFRACTION100
1.7859-1.82480.20914890.17269304X-RAY DIFFRACTION100
1.8248-1.86720.18394860.17019216X-RAY DIFFRACTION100
1.8672-1.91390.19584930.16669285X-RAY DIFFRACTION100
1.9139-1.96570.17014880.15189229X-RAY DIFFRACTION100
1.9657-2.02350.17684940.15349372X-RAY DIFFRACTION100
2.0235-2.08880.17994870.1529207X-RAY DIFFRACTION99
2.0888-2.16350.18494810.14749232X-RAY DIFFRACTION100
2.1635-2.25010.16824900.14469254X-RAY DIFFRACTION100
2.2501-2.35250.17064870.15359259X-RAY DIFFRACTION99
2.3525-2.47650.16934870.1579278X-RAY DIFFRACTION99
2.4765-2.63170.20234880.16029230X-RAY DIFFRACTION100
2.6317-2.83490.1924840.16519212X-RAY DIFFRACTION99
2.8349-3.12010.17554860.16439258X-RAY DIFFRACTION99
3.1201-3.57150.16824790.1479165X-RAY DIFFRACTION99
3.5715-4.49920.1374750.12329108X-RAY DIFFRACTION98
4.4992-48.47250.13984880.13229262X-RAY DIFFRACTION100
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)
12.6681.0386-0.50452.79930.45562.5984-0.0492-0.2345-0.1720.1605-0.0261-0.0040.5224-0.1530.04380.2654-0.03160.00090.20030.01710.2145-29.21478.779664.5616
22.17680.4160.59591.94620.29562.6558-0.04840.04350.2999-0.05470.06540.0742-0.2251-0.0733-0.01720.1645-0.0095-0.01160.1637-0.00740.2365-27.192822.071957.5624
31.5223-0.2365-0.29171.57040.26292.3753-0.06840.2312-0.0129-0.12110.05230.01010.0523-0.21960.00630.2285-0.057-0.0090.2292-0.02460.1791-30.40912.997547.8723
48.2453-2.5994-0.34833.23560.35264.2036-0.0541-0.0074-1.1751-0.40360.021-0.28140.8841-0.4841-0.04470.4502-0.16150.06990.27-0.0510.4489-39.0523-2.392558.0254
51.59430.8049-0.60171.9656-0.10232.2331-0.38110.2104-0.6648-0.18540.0919-0.10530.7814-0.34050.11790.3784-0.07080.09220.1705-0.01020.4007-31.66841.512459.494
61.46223.2735-0.38837.4658-0.47543.5517-0.0979-0.2997-0.84080.59240.0495-0.6180.54910.5961-0.12680.36190.09660.01510.25050.04160.5343-18.85943.718659.0342
71.8152-0.04210.59421.4423-0.3452.4057-0.05970.16390.1477-0.24270.1105-0.29130.21290.1822-0.05250.2763-0.03470.04280.2923-0.04360.2297-20.06510.667343.9277
81.6095-1.5288-0.67758.34883.23223.30350.16560.17790.051-0.0694-0.1711-0.41310.1012-0.1052-0.04540.18520.00730.0040.1560.01240.1936-9.005112.914816.6575
92.14670.19710.23472.54830.36522.67120.1255-0.1635-0.1350.438-0.1407-0.17170.14340.10050.02170.2314-0.0145-0.040.17070.01860.2278-6.624416.145527.0609
101.8166-0.0650.63931.25780.00282.3437-0.0578-0.03760.25960.1252-0.05270.0779-0.3904-0.1040.09230.23480.0193-0.00710.13880.00160.2471-11.362728.620920.6335
111.55910.1390.86231.49210.23872.0494-0.11610.17680.3028-0.2086-0.03330.0326-0.36910.02810.14090.26920.0071-0.0110.18170.0440.2641-11.553329.858510.9892
121.4050.3757-0.48821.2115-0.46931.9280.0248-0.01210.06710.0574-0.0330.0463-0.0526-0.1583-0.00670.15530.008-0.0050.1646-0.00560.1647-19.615412.093620.8012
131.58340.2417-0.58181.88260.27892.54230.09690.0018-0.0671-0.0459-0.0431-0.10060.1387-0.0256-0.03330.17390.0035-0.00380.13810.00470.1903-13.05918.85121.4272
141.10850.79890.37446.7847-1.4432.10330.05250.2454-0.2574-0.1055-0.2255-0.82710.0760.26570.20010.20130.04250.03390.22670.00330.3117-3.221811.065513.2814
152.667-0.00440.30281.1987-0.02091.7003-0.11750.4350.1615-0.34440.025-0.0548-0.11830.14620.08450.30640.01690.00160.26920.02270.2332-13.482519.27112.6443
161.47450.47050.31432.8912-0.10161.7131-0.15490.30890.0105-0.22790.2295-0.19820.38320.0201-0.05520.3644-0.01370.01770.3640.01460.2054-26.39245.0011-15.2497
172.2639-0.0549-0.01193.0283-0.49022.5059-0.17670.50170.1817-0.41340.18460.0880.2278-0.3122-0.02280.3073-0.0428-0.04110.38270.04850.1969-33.37969.7392-16.2505
181.04130.19090.36791.5003-0.52412.3064-0.09290.0240.1812-0.08880.08820.2396-0.1539-0.5437-0.00150.20530.0378-0.02990.34080.05120.2228-37.53315.8321-4.642
191.0223-0.552-0.09141.578-0.4892.223-0.1363-0.09640.04320.1360.24380.2567-0.0242-0.5827-0.08630.20790.0180.00230.35180.05660.2129-37.116211.00913.9061
203.1068-0.4987-0.74131.26330.53992.50730.00010.12240.3927-0.21410.1002-0.1372-0.05650.0454-0.07790.29050.0360.02120.29120.0490.2434-22.59098.7476-2.943
214.57251.6586-1.72234.7318-1.6114.6712-0.0936-0.1055-0.1771-0.054-0.1218-0.30020.44750.88040.15850.33320.09080.02530.42230.00440.2971-12.42682.7097-8.4615
221.7327-0.17220.53034.3977-1.86942.8741-0.08220.0249-0.1275-0.20230.0257-0.37040.35730.20480.03430.32690.05410.01980.28350.01190.2341-23.62842.2527-5.3177
233.69571.0029-0.01875.3456-1.38413.79720.15870.4815-0.1041-0.1568-0.2478-0.30110.70610.40590.04780.44370.13690.06550.40910.03290.2887-17.9114-0.2143-14.0329
246.2457-2.1216-1.21683.23480.4883.75270.08450.3288-0.66980.0714-0.14960.35890.9351-0.36580.02960.5793-0.0988-0.0410.3033-0.01050.2894-31.947-5.2419-8.1672
252.05360.71970.13680.8033-0.16061.0681-0.2516-0.14-0.0285-0.21010.12560.19840.3393-0.28460.11510.2867-0.02010.00790.30010.02150.2029-34.70622.10486.9529
262.3904-0.49580.31851.57860.4142.178-0.02330.1787-0.19350.011-0.04940.12480.1683-0.04830.06890.1682-0.02690.02480.2315-0.01940.197-46.7772-1.39327.4516
271.46290.30220.31981.4930.9852.9978-0.01890.06730.1067-0.1145-0.17950.3479-0.2835-0.55170.15970.19110.05020.0030.3222-0.02340.2584-55.493710.852130.1532
282.72090.5023-0.69862.3611-0.1092.68940.0289-0.30130.34670.2234-0.09330.2764-0.411-0.19180.02420.22770.02650.03560.2795-0.05850.2461-50.09218.589343.6181
291.2841-0.2569-0.87280.82210.54561.61360.02410.0011-0.020.0176-0.05290.0389-0.0567-0.02640.01980.1657-0.00950.00780.194-0.00070.1631-35.88455.759629.3642
301.5788-0.15040.42491.7224-0.77772.7130.0375-0.0467-0.13610.105-0.00150.07270.18040.0337-0.03470.195-0.00170.0170.2220.01350.1901-39.90922.346833.7074
311.6514-0.0890.23423.7989-2.61695.2301-0.05460.0721-0.31570.0071-0.03130.09990.28970.00770.0830.2004-0.01370.02980.2236-0.01060.2522-36.8629-4.895526.3897
324.2892-1.8232-1.57083.21040.86832.7649-0.0241-0.1273-0.47320.4343-0.12890.33450.1916-0.19130.14350.2758-0.05170.03810.2150.02960.248-47.1139-5.249138.813
331.1920.9525-0.3631.8296-0.0821.37730.1049-0.29640.08240.2568-0.09480.1435-0.0219-0.1663-0.0240.2341-0.01890.03240.2749-0.00920.204-46.64939.621246.9976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 204 )
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 261 )
7X-RAY DIFFRACTION7chain 'A' and (resid 262 through 273 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 78 )
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 102 )
10X-RAY DIFFRACTION10chain 'B' and (resid 103 through 140 )
11X-RAY DIFFRACTION11chain 'B' and (resid 141 through 183 )
12X-RAY DIFFRACTION12chain 'B' and (resid 184 through 219 )
13X-RAY DIFFRACTION13chain 'B' and (resid 220 through 249 )
14X-RAY DIFFRACTION14chain 'B' and (resid 250 through 261 )
15X-RAY DIFFRACTION15chain 'B' and (resid 262 through 273 )
16X-RAY DIFFRACTION16chain 'C' and (resid 69 through 92 )
17X-RAY DIFFRACTION17chain 'C' and (resid 93 through 118 )
18X-RAY DIFFRACTION18chain 'C' and (resid 119 through 156 )
19X-RAY DIFFRACTION19chain 'C' and (resid 157 through 183 )
20X-RAY DIFFRACTION20chain 'C' and (resid 184 through 204 )
21X-RAY DIFFRACTION21chain 'C' and (resid 205 through 219 )
22X-RAY DIFFRACTION22chain 'C' and (resid 220 through 233 )
23X-RAY DIFFRACTION23chain 'C' and (resid 234 through 249 )
24X-RAY DIFFRACTION24chain 'C' and (resid 250 through 261 )
25X-RAY DIFFRACTION25chain 'C' and (resid 262 through 273 )
26X-RAY DIFFRACTION26chain 'D' and (resid 68 through 102 )
27X-RAY DIFFRACTION27chain 'D' and (resid 103 through 166 )
28X-RAY DIFFRACTION28chain 'D' and (resid 167 through 184 )
29X-RAY DIFFRACTION29chain 'D' and (resid 185 through 219 )
30X-RAY DIFFRACTION30chain 'D' and (resid 220 through 233 )
31X-RAY DIFFRACTION31chain 'D' and (resid 234 through 249 )
32X-RAY DIFFRACTION32chain 'D' and (resid 250 through 261 )
33X-RAY DIFFRACTION33chain 'D' and (resid 262 through 273 )

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