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- PDB-6nvy: Crystal structure of penicillin G acylase from Bacillus thermotolerans -

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Basic information

Entry
Database: PDB / ID: 6nvy
TitleCrystal structure of penicillin G acylase from Bacillus thermotolerans
Components(Penicillin G acylase) x 2
KeywordsHYDROLASE / penicillin / acylase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Penicillin G acylase
Similarity search - Component
Biological speciesQuasibacillus thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsBlankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP1934 Germany
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2019
Title: Crystal structures and protein engineering of three different penicillin G acylases from Gram-positive bacteria with different thermostability.
Authors: Mayer, J. / Pippel, J. / Gunther, G. / Muller, C. / Lauermann, A. / Knuuti, T. / Blankenfeldt, W. / Jahn, D. / Biedendieck, R.
History
DepositionFeb 5, 2019Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.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: Penicillin G acylase
B: Penicillin G acylase
C: Penicillin G acylase
D: Penicillin G acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,47417
Polymers172,9014
Non-polymers57313
Water12,989721
1
A: Penicillin G acylase
B: Penicillin G acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7839
Polymers86,4502
Non-polymers3337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-115 kcal/mol
Surface area27830 Å2
MethodPISA
2
C: Penicillin G acylase
D: Penicillin G acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6918
Polymers86,4502
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-114 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.996, 172.996, 209.566
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Penicillin G acylase


Mass: 24785.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Quasibacillus thermotolerans (bacteria)
Gene: QY95_01219 / Production host: Bacillus megaterium (bacteria) / References: UniProt: A0A0F5I5V4
#2: Protein Penicillin G acylase


Mass: 61664.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Quasibacillus thermotolerans (bacteria)
Gene: QY95_01219 / Production host: Bacillus megaterium (bacteria) / References: UniProt: A0A0F5I5V4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 309 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 18 mM CaCl2, 90 mM sodium acetate, 27% (v/v) 2-methyl-2,4-pentanediol, 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.27→49.45 Å / Num. obs: 108061 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.037 / Rrim(I) all: 0.12 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.27-2.3110.51.54953640.7240.5011.628100
12.43-49.4510.70.0376320.9990.0120.03996.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIXdev_3386refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVX
Resolution: 2.27→43.249 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.1997 5148 4.77 %
Rwork0.1723 --
obs0.1737 107998 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 188.33 Å2 / Biso mean: 60.8634 Å2 / Biso min: 23.1 Å2
Refinement stepCycle: final / Resolution: 2.27→43.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11820 0 26 721 12567
Biso mean--82.27 52.85 -
Num. residues----1454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.27-2.29580.3572140.288233733587100
2.2958-2.32280.29441250.27534853610100
2.3228-2.35120.32711610.261634613622100
2.3512-2.38090.31861680.254534143582100
2.3809-2.41220.3191150.24434893604100
2.4122-2.44530.26021640.242234403604100
2.4453-2.48020.24891480.22734403588100
2.4802-2.51720.28291540.226734653619100
2.5172-2.55660.24721800.218334243604100
2.5566-2.59850.24161670.214734353602100
2.5985-2.64330.21871880.205434163604100
2.6433-2.69130.23251490.200834543603100
2.6913-2.74310.22091970.197133863583100
2.7431-2.79910.20712580.184433523610100
2.7991-2.85990.20841690.179134193588100
2.8599-2.92640.19591700.176434183588100
2.9264-2.99960.21771840.176234183602100
2.9996-3.08070.19621600.174934543614100
3.0807-3.17130.20051870.167933903577100
3.1713-3.27360.19322340.169433873621100
3.2736-3.39060.17531770.15634443621100
3.3906-3.52630.15751660.149934323598100
3.5263-3.68670.18031500.137834563606100
3.6867-3.88090.15231350.136234263561100
3.8809-4.12390.1571350.135534893624100
4.1239-4.4420.14831440.127134433587100
4.442-4.88850.16371560.135834753631100
4.8885-5.59460.16991600.15734203580100
5.5946-7.04370.22222100.197633933603100
7.0437-43.25680.21212230.19893352357599
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)
12.54151.665-0.20323.38010.92914.7602-0.04290.1502-0.1694-0.16210.10020.86740.0803-1.1459-0.03210.38170.06230.06750.7281-0.01060.9811-20.277629.9781114.2512
22.29930.9688-1.02963.3411-0.70822.5630.28220.28630.4489-0.1515-0.12890.9613-0.5808-0.4971-0.15270.48020.2167-0.00560.56070.01660.6899-10.809844.2011106.1243
33.13191.0961-0.45384.3619-0.00612.06510.09970.89550.4045-0.67350.10720.5611-0.4908-0.354-0.15790.64170.2048-0.06360.65950.17250.4766-1.381846.867393.6967
43.5554-0.8908-1.00634.01320.98183.58030.44010.531-0.0602-0.2178-0.03481.0418-0.5581-1.090.0410.50340.2101-0.09060.77060.09321.0104-19.400442.3104103.8779
52.94730.0041-1.09193.28441.33623.16970.4281-0.05210.6171-0.0637-0.19961.0021-0.7425-0.2765-0.10440.65750.27380.0420.55610.11020.9183-12.459153.4297110.2738
64.3855-0.3541-0.97462.75290.49592.35110.09830.17120.6046-0.401-0.05610.5441-0.264-0.2131-0.13510.49650.069-0.05470.43570.02790.40381.314140.122399.5355
72.06331.5338-0.69373.8109-1.26874.66440.16680.03030.2188-0.3881-0.0218-0.1234-0.53780.3185-0.170.537-0.05330.07930.4724-0.01460.29830.391842.932897.8369
88.49313.1672-1.23738.1593-2.77536.8888-0.11510.366-0.3762-0.7391-0.2588-0.87820.15570.98390.16650.45390.01580.09670.5981-0.03060.328536.183534.992697.6821
97.18640.011-0.80773.0141-0.38425.9616-0.24050.6486-1.3344-0.44870.0543-0.26811.1169-0.16060.16980.57750.01780.01020.4001-0.12710.380220.97918.9533102.0915
101.02030.2394-0.47181.7352-0.35321.64660.01550.1998-0.1451-0.1291-0.03740.4258-0.0495-0.30930.01160.30780.0192-0.03840.4029-0.03910.4089-0.436226.7836107.4472
111.13410.3139-0.78571.3672-0.37181.81140.18380.29480.2423-0.3722-0.04550.3891-0.4761-0.1817-0.12750.56930.1061-0.09750.530.03680.34755.438442.417291.168
120.99760.5323-0.72262.3373-0.27691.7287-0.0210.3347-0.1646-0.3434-0.00520.10680.0155-0.07230.01970.3270.0309-0.04890.3493-0.03150.242814.125123.267999.8556
134.55210.4936-0.14982.03610.81941.8533-0.0008-0.3878-0.26940.5669-0.0092-0.13970.09730.26530.02210.5691-0.0074-0.0360.39920.04530.249223.731924.846128.0979
142.11892.0609-1.35895.2393-4.47759.47370.1824-0.0808-0.05590.4855-0.0287-0.3367-1.03040.5353-0.17890.4275-0.04280.00270.4058-0.090.270130.540237.7147116.4375
153.7549-0.11551.28023.42121.40199.08230.0553-0.0791-0.04590.24330.1464-0.4684-0.10310.9498-0.23580.2959-0.0457-0.00920.32440.02680.234735.249931.4192117.2746
161.8321-0.2376-0.02991.806-0.10211.24090.0227-0.14150.16530.3682-0.02440.3863-0.2168-0.14460.02050.46420.0020.12410.3561-0.01720.37593.577934.682122.5049
174.8035-0.80980.78233.87820.43884.0762-0.0238-0.4276-0.2960.3430.0051.2242-0.1287-0.68640.04840.4810.00070.21010.5618-0.00880.7714-12.89731.6332121.9193
182.7892-2.04934.17672.9527-1.38818.23430.11620.33760.6629-0.03840.0137-0.9369-0.51111.0312-0.25520.4349-0.16050.04070.5196-0.11730.958636.0608102.5873145.3327
192.7578-1.10661.86353.38570.39261.93470.06530.44560.6215-0.1028-0.1715-0.638-0.22630.56070.08850.278-0.10730.11470.6701-0.01270.77143.694787.3501137.0065
204.93671.17033.80025.28881.62383.0294-0.0596-0.0096-0.74010.39830.1371-0.48550.67050.8833-0.10840.48010.09560.0710.7864-0.0810.788444.696368.6901131.1299
216.2789-3.94821.3083.1893-1.81662.48180.39010.99270.7637-1.3837-0.399-1.7314-0.17610.96680.22950.6543-0.22580.28590.88-0.00430.733838.506786.091118.8685
222.7525-1.70912.1173.123-1.34484.9757-0.40610.44271.0522-0.20070.1268-0.8569-0.62260.86170.21850.4442-0.22650.17230.8041-0.00611.008246.341995.7939134.8119
231.9607-1.72792.31964.095-2.9145.4916-0.06460.09030.4883-0.0961-0.1127-0.90650.38080.84240.02420.3976-0.06050.09470.9345-0.0820.905152.505883.8814141.3336
245.32393.71970.86999.570.1193.7820.0340.4666-0.2268-0.3778-0.1731-0.52930.3740.34520.17680.3060.06290.07730.4807-0.0360.455734.157378.9593130.3072
257.60917.1572-4.03659.4876-4.26197.255-0.02020.3279-0.4739-0.5670.085-1.13320.71290.4566-0.11540.48490.10380.02380.4484-0.09640.54722.520552.3615128.4339
269.3708-3.9406-4.06673.12224.97069.4201-0.31180.3446-0.7379-0.6778-0.1346-0.08760.5377-0.5260.47130.5806-0.00560.08220.36370.00710.518312.841351.0588128.1923
272.93661.09060.17956.09870.00075.60770.26070.49880.3906-0.7185-0.37490.6321-0.4845-0.59930.09310.39090.0556-0.01760.3851-0.01740.44315.927672.3296132.6565
281.1927-0.3718-0.30381.55710.79351.6758-0.05590.06330.2461-0.16860.0471-0.2508-0.18290.2843-0.05130.3097-0.02620.02060.31810.04410.502323.43487.0006138.288
290.8202-0.1155-0.0731.54361.25261.9628-0.02920.21530.0241-0.27450.2755-0.48950.05490.6675-0.13710.4143-0.01080.13460.56910.00050.542734.173974.0123121.8773
301.1662-0.06660.29181.11160.28311.1506-0.05610.0822-0.0397-0.13230.0222-0.03280.0321-0.01450.03510.27710.00470.0370.24950.02060.398512.208174.6647136.1728
312.99990.19210.5232.64221.13534.37620.0085-0.5235-0.45480.58550.03390.11890.4563-0.40060.05810.41340.08250.03890.43340.14490.40210.014463.6931163.7833
321.1816-0.5461-0.38921.35660.79864.6885-0.0022-0.1463-0.47510.0565-0.0348-0.01970.7970.0088-0.01650.50710.0270.01790.30140.0790.580713.221254.0233147.3964
331.81560.6403-0.05892.3405-0.13221.9929-0.0551-0.3389-0.10480.17780.0227-0.50880.21960.48440.06530.28430.055-0.03540.4232-0.02390.484728.242479.4624153.2395
345.84270.9521-0.5883.3374-0.49892.4653-0.0982-0.4591.02150.32050.1447-0.3877-0.75010.7258-0.02290.5042-0.0784-0.09440.5743-0.14370.745233.827295.2749152.8968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 25 )A7 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 61 )A26 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 89 )A62 - 89
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 117 )A90 - 117
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 133 )A118 - 133
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 152 )A134 - 152
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 168 )A153 - 168
8X-RAY DIFFRACTION8chain 'A' and (resid 169 through 180 )A169 - 180
9X-RAY DIFFRACTION9chain 'A' and (resid 181 through 197 )A181 - 197
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 81 )B1 - 81
11X-RAY DIFFRACTION11chain 'B' and (resid 82 through 187 )B82 - 187
12X-RAY DIFFRACTION12chain 'B' and (resid 188 through 281 )B188 - 281
13X-RAY DIFFRACTION13chain 'B' and (resid 282 through 345 )B282 - 345
14X-RAY DIFFRACTION14chain 'B' and (resid 346 through 378 )B346 - 378
15X-RAY DIFFRACTION15chain 'B' and (resid 379 through 424 )B379 - 424
16X-RAY DIFFRACTION16chain 'B' and (resid 425 through 493 )B425 - 493
17X-RAY DIFFRACTION17chain 'B' and (resid 494 through 536 )B494 - 536
18X-RAY DIFFRACTION18chain 'C' and (resid 7 through 25 )C7 - 25
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 61 )C26 - 61
20X-RAY DIFFRACTION20chain 'C' and (resid 62 through 74 )C62 - 74
21X-RAY DIFFRACTION21chain 'C' and (resid 75 through 89 )C75 - 89
22X-RAY DIFFRACTION22chain 'C' and (resid 90 through 117 )C90 - 117
23X-RAY DIFFRACTION23chain 'C' and (resid 118 through 133 )C118 - 133
24X-RAY DIFFRACTION24chain 'C' and (resid 134 through 152 )C134 - 152
25X-RAY DIFFRACTION25chain 'C' and (resid 153 through 168 )C153 - 168
26X-RAY DIFFRACTION26chain 'C' and (resid 169 through 180 )C169 - 180
27X-RAY DIFFRACTION27chain 'C' and (resid 181 through 197 )C181 - 197
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 81 )D1 - 81
29X-RAY DIFFRACTION29chain 'D' and (resid 82 through 187 )D82 - 187
30X-RAY DIFFRACTION30chain 'D' and (resid 188 through 312 )D188 - 312
31X-RAY DIFFRACTION31chain 'D' and (resid 313 through 345 )D313 - 345
32X-RAY DIFFRACTION32chain 'D' and (resid 346 through 424 )D346 - 424
33X-RAY DIFFRACTION33chain 'D' and (resid 425 through 493 )D425 - 493
34X-RAY DIFFRACTION34chain 'D' and (resid 494 through 536 )D494 - 536

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