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- PDB-5n1j: Crystal structure of the polysaccharide deacetylase Bc1974 from B... -

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Basic information

Entry
Database: PDB / ID: 5n1j
TitleCrystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus
ComponentsPeptidoglycan N-acetylglucosamine deacetylase
KeywordsHYDROLASE / CE4 fold / polysaccharide deacetylase / Bacillus cereus / PgdA
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
ACETATE ION / Peptidoglycan-N-acetylglucosamine deacetylase BC_1974
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGiastas, P. / Andreou, A. / Balomenou, S. / Bouriotis, V. / 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 1.1Jan 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_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.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.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

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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)94,62520
Polymers93,6304
Non-polymers99416
Water12,629701
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-153 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.280, 117.668, 99.768
Angle α, β, γ (deg.)90.00, 102.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptidoglycan N-acetylglucosamine deacetylase / Bc1974


Mass: 23407.607 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: We determined the residues 67-273. Each chain contains the zinc ion coordinating a conserved His-His-Asp motif.
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
Details: We determined the residues 67-273. Each chain contains the zinc ion coordinating a conserved His-His-Asp motif.
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC_1974 / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 100 mM Sodium citrate, 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: Feb 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.65 Å / Num. obs: 104340 / % possible obs: 99.8 % / Observed criterion σ(I): 2.1 / Redundancy: 6.7 % / Biso Wilson estimate: 25.1 Å2 / CC1/2: 0.99 / Rsym value: 0.082 / Net I/σ(I): 2.43
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 6.5 % / Num. unique obs: 10932 / CC1/2: 0.8 / Rsym value: 0.89 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C1G
Resolution: 1.8→45.266 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.96
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 5219 5 %Random selection
Rwork0.1733 ---
obs0.1748 104340 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 52 701 7357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116856
X-RAY DIFFRACTIONf_angle_d1.0149241
X-RAY DIFFRACTIONf_dihedral_angle_d12.0362517
X-RAY DIFFRACTIONf_chiral_restr0.04958
X-RAY DIFFRACTIONf_plane_restr0.0051208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.31211600.26543255X-RAY DIFFRACTION100
1.8205-1.84190.32511800.26213279X-RAY DIFFRACTION100
1.8419-1.86430.33511750.26583350X-RAY DIFFRACTION100
1.8643-1.88790.33611620.25343234X-RAY DIFFRACTION100
1.8879-1.91280.27981620.23683337X-RAY DIFFRACTION100
1.9128-1.9390.28411560.23333319X-RAY DIFFRACTION100
1.939-1.96670.2661760.20983242X-RAY DIFFRACTION100
1.9667-1.9960.24281930.21233352X-RAY DIFFRACTION100
1.996-2.02720.21861940.19693251X-RAY DIFFRACTION100
2.0272-2.06050.22791790.19693304X-RAY DIFFRACTION100
2.0605-2.0960.23561630.19713337X-RAY DIFFRACTION100
2.096-2.13410.23361800.18413256X-RAY DIFFRACTION100
2.1341-2.17520.2271630.1853337X-RAY DIFFRACTION100
2.1752-2.21960.2091430.1843312X-RAY DIFFRACTION100
2.2196-2.26780.21111840.1933296X-RAY DIFFRACTION100
2.2678-2.32060.24731660.18293314X-RAY DIFFRACTION100
2.3206-2.37860.21191790.18273328X-RAY DIFFRACTION100
2.3786-2.44290.23121800.17743243X-RAY DIFFRACTION100
2.4429-2.51480.22451710.18183344X-RAY DIFFRACTION100
2.5148-2.5960.20971700.17633264X-RAY DIFFRACTION100
2.596-2.68870.19961530.18693328X-RAY DIFFRACTION100
2.6887-2.79640.22721680.18833339X-RAY DIFFRACTION100
2.7964-2.92360.25381750.19123277X-RAY DIFFRACTION100
2.9236-3.07770.2071990.18693284X-RAY DIFFRACTION100
3.0777-3.27050.22111910.17793295X-RAY DIFFRACTION100
3.2705-3.52290.20211790.17373301X-RAY DIFFRACTION100
3.5229-3.87730.15461760.15663346X-RAY DIFFRACTION100
3.8773-4.43790.15351710.13243301X-RAY DIFFRACTION99
4.4379-5.58970.15421760.12863353X-RAY DIFFRACTION100
5.5897-45.280.15591950.14163343X-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)
12.480.5519-0.24713.1447-0.44792.7098-0.1050.12150.0213-0.38630.1481-0.13860.23090.2077-0.03730.16340.00440.02540.1589-0.02740.15852.339-5.703439.7214
22.0408-0.5437-0.9033.17071.78943.18060.06830.01920.02380.1069-0.07680.20760.0227-0.22770.04320.1547-0.00660.00890.20460.00740.2301-3.1447-0.174152.8157
31.48531.00530.8557.93024.78113.4150.0284-0.0656-0.00350.33720.01930.11950.1012-0.1555-0.08580.2069-0.02310.02310.17340.01920.2087-5.2689-7.104755.9758
41.13920.09040.33931.85050.08951.94130.00930.0263-0.03070.115-0.00890.02080.00640.0023-0.01990.15780.00020.00440.1694-0.01520.21443.30713.265753.0593
59.4394-1.92273.14116.8164-1.81689.1544-0.31670.82860.3268-0.841-0.077-0.7454-0.61280.93310.25250.3328-0.05180.0960.25740.05050.27778.337911.016732.381
61.1847-0.41520.57811.86540.17512.1519-0.08270.20120.0929-0.23620.0215-0.52590.02080.60210.06460.1702-0.00940.0760.3390.00740.32912.04921.099439.9562
72.1481-0.0744-0.11383.2532-0.18753.5181-0.0053-0.2181-0.23640.2660.0855-0.3094-0.15680.4643-0.04430.17980.0128-0.01840.236-0.03520.266612.48962.18158.7111
82.38950.44450.09612.63540.69552.8694-0.07880.0243-0.13810.23340.1596-0.33720.43060.4155-0.0790.36130.0788-0.05950.2354-0.00240.207817.97316.699583.2254
94.82250.09880.27083.3223-0.44482.82940.0103-0.3161-0.43590.13230.00080.00970.9251-0.1104-0.0250.5261-0.0203-0.01010.21870.05890.19677.6107-1.25986.7221
102.0486-0.2738-0.08792.8260.31172.4447-0.0226-0.1854-0.07720.46620.04340.16910.1645-0.09130.00090.3135-0.02490.00380.19610.03640.15362.958311.583790.2647
110.8293-1.22860.59975.5847-0.0920.610.0027-0.1279-0.22460.6036-0.00080.41950.05020.0292-0.01730.5363-0.00280.06620.24250.05530.22511.57926.549996.3174
121.7498-0.16180.10242.6675-0.1131.65230.0446-0.29450.03610.44810.07530.1722-0.1632-0.0721-0.12220.4510.00380.03110.25760.03160.18915.144817.007695.9998
130.7885-0.09130.30941.73550.57383.7492-0.05340.0021-0.0030.23370.012-0.0257-0.027-0.05570.03190.17720.0163-0.01950.16090.00640.180713.009617.285378.6586
141.0585-0.0405-0.99992.2197-0.44471.0462-0.0526-0.11210.0821-0.04860.0144-0.3626-0.14640.1680.07190.24380.0106-0.07050.2465-0.01160.236318.255317.771983.236
157.46261.82481.68074.53170.60174.0761-0.1505-0.2470.0414-0.04340.0906-0.38910.35640.42720.01090.24210.0626-0.00930.2431-0.00020.163920.614710.714675.2375
166.29080.1351-2.61564.104-0.26426.0608-0.3885-0.6061-0.46750.50210.083-0.75340.59480.9530.29520.36060.0786-0.14810.3001-0.02080.333625.04712.73889.5295
175.3384-0.748-0.20693.0165-0.97834.61420.2128-0.18490.33710.6994-0.2002-0.3394-0.23190.2645-0.07390.44410.0097-0.05790.2526-0.03710.199313.243423.139897.1948
182.8913-0.7958-0.73262.19680.0492.586-0.1648-0.36570.10320.30750.1181-0.5577-0.09360.45780.03060.38570.0072-0.0980.3063-0.08160.30122.804645.99196.7275
193.40130.72310.34483.9859-0.15243.1096-0.2208-0.42610.26510.64970.3769-0.0676-0.2455-0.0586-0.1330.48360.062-0.01550.2812-0.05670.20310.783251.1899.855
201.78790.15430.20431.83690.22671.6111-0.0517-0.12420.02760.16080.0426-0.027-0.22430.0037-0.01030.3770.01580.03710.2058-0.04610.17587.388841.970489.668
210.53290.64640.11297.01744.4093.1433-0.0774-0.0692-0.0005-0.04760.1440.0257-0.635-0.1988-0.08290.39260.04450.00560.2241-0.02220.19353.873248.904388.1612
221.9186-1.5304-1.43024.2872.47112.14270.0202-0.0820.27590.04220.2612-0.0153-0.6176-0.0375-0.24460.5162-0.0252-0.01560.1991-0.0330.203612.261949.902486.4333
231.2330.01520.19341.9429-1.87094.5555-0.04620.04650.0020.08430.04610.07070.0663-0.228-0.00730.32630.01040.00780.2062-0.03320.18696.927136.669378.6814
241.82630.21540.69591.9154-0.00231.94030.0121-0.13760.00120.5598-0.0397-0.3074-0.1830.2034-0.05460.42870.0178-0.03510.2116-0.06140.182317.046435.333990.7885
254.00690.1829-0.17446.5011-0.30288.74140.0186-0.3057-0.04710.81060.2312-0.96280.64480.8988-0.17320.42890.1073-0.15240.4582-0.09260.473428.247331.0028100.7078
266.1505-1.2733-2.76134.94310.8296.2146-0.1912-0.0681-0.08750.13410.1496-0.8460.2850.56980.04060.26960.0127-0.03460.3257-0.06810.331324.82437.257289.8296
270.90640.0803-1.18142.5919-0.29731.59010.20220.1388-0.23670.62690.0868-0.8680.20340.8304-0.1320.3210.0522-0.15480.5292-0.11030.418928.120838.9091100.0284
289.0592-2.14363.11764.61120.57394.4606-0.44120.26231.2074-0.33310.0332-1.2939-0.40221.07960.35210.3423-0.08330.08210.4969-0.02550.499228.963746.698287.0707
292.11150.5304-0.15374.3147-0.90141.27490.2710.30880.0891-0.15270.026-0.1882-0.20830.2361-0.27080.3417-0.03350.05150.2676-0.06040.222817.399739.784976.239
301.7134-0.1541-0.10322.38430.15871.9172-0.11590.03150.1369-0.10780.0743-0.1735-0.08190.28830.01640.1389-0.03760.01550.19930.01880.20438.754435.441252.7859
316.82140.0704-2.4523.0670.16965.45260.0907-0.24930.41970.0598-0.03260.1467-0.5653-0.2054-0.0660.17030.0052-0.00770.18620.01840.2593-1.935542.990155.4831
323.073-0.0190.09812.07610.23612.0693-0.0188-0.1956-0.0866-0.02760.04840.3901-0.01-0.2151-0.02440.10450.0178-0.00710.16390.01980.2012-7.590730.192554.8667
330.9115-0.65430.14063.5686-0.12381.14020.07920.09550.0267-0.17430.00170.4654-0.0548-0.2237-0.08680.1317-0.0054-0.03850.17130.02030.2541-9.421934.652948.9021
343.7634-0.60310.91742.8446-0.99384.70950.23030.1252-0.6249-0.1032-0.1820.53330.576-0.4730.00010.2174-0.0255-0.05780.22-0.0170.3258-11.152119.455850.3764
350.97110.08991.07311.10180.30812.7843-0.02740.0420.01950.03910.01450.0672-0.00250.0126-0.0330.1247-0.01350.01410.18410.00970.19927.199124.606559.1787
362.2381-0.4714-0.59651.62820.18211.1437-0.06820.0448-0.0789-0.00830.0867-0.17510.08080.2217-0.0180.1571-0.01260.01760.24540.00080.22089.147524.191252.4838
371.8249-1.1963-1.47962.97271.33212.9492-0.04160.07820.1286-0.04870.0186-0.3943-0.21370.41460.06470.1174-0.03680.00080.27970.01030.252115.329531.30558.028
382.0219-0.57171.5594.18980.10173.2338-0.00540.72450.2035-0.4201-0.0212-0.3495-0.14510.35320.13250.2253-0.03460.06290.28180.02750.184310.367329.739342.6835
393.58331.0504-0.67424.458-1.26984.42050.08-0.0159-0.202-0.2771-0.2015-0.0950.25770.21950.15350.19510.0103-0.01960.2042-0.02680.2471-2.509718.714943.4422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 139 )
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 218 )
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 260 )
7X-RAY DIFFRACTION7chain 'A' and (resid 261 through 272 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 101 )
9X-RAY DIFFRACTION9chain 'B' and (resid 102 through 117 )
10X-RAY DIFFRACTION10chain 'B' and (resid 118 through 139 )
11X-RAY DIFFRACTION11chain 'B' and (resid 140 through 155 )
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 182 )
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 218 )
14X-RAY DIFFRACTION14chain 'B' and (resid 219 through 232 )
15X-RAY DIFFRACTION15chain 'B' and (resid 233 through 248 )
16X-RAY DIFFRACTION16chain 'B' and (resid 249 through 260 )
17X-RAY DIFFRACTION17chain 'B' and (resid 261 through 272 )
18X-RAY DIFFRACTION18chain 'C' and (resid 68 through 101 )
19X-RAY DIFFRACTION19chain 'C' and (resid 102 through 117 )
20X-RAY DIFFRACTION20chain 'C' and (resid 118 through 139 )
21X-RAY DIFFRACTION21chain 'C' and (resid 140 through 155 )
22X-RAY DIFFRACTION22chain 'C' and (resid 156 through 165 )
23X-RAY DIFFRACTION23chain 'C' and (resid 166 through 182 )
24X-RAY DIFFRACTION24chain 'C' and (resid 183 through 203 )
25X-RAY DIFFRACTION25chain 'C' and (resid 204 through 218 )
26X-RAY DIFFRACTION26chain 'C' and (resid 219 through 232 )
27X-RAY DIFFRACTION27chain 'C' and (resid 233 through 248 )
28X-RAY DIFFRACTION28chain 'C' and (resid 249 through 260 )
29X-RAY DIFFRACTION29chain 'C' and (resid 261 through 272 )
30X-RAY DIFFRACTION30chain 'D' and (resid 68 through 101 )
31X-RAY DIFFRACTION31chain 'D' and (resid 102 through 117 )
32X-RAY DIFFRACTION32chain 'D' and (resid 118 through 139 )
33X-RAY DIFFRACTION33chain 'D' and (resid 140 through 165 )
34X-RAY DIFFRACTION34chain 'D' and (resid 166 through 182 )
35X-RAY DIFFRACTION35chain 'D' and (resid 183 through 218 )
36X-RAY DIFFRACTION36chain 'D' and (resid 219 through 232 )
37X-RAY DIFFRACTION37chain 'D' and (resid 233 through 248 )
38X-RAY DIFFRACTION38chain 'D' and (resid 249 through 260 )
39X-RAY DIFFRACTION39chain 'D' and (resid 261 through 272 )

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