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- PDB-1obn: ISOPENICILLIN N SYNTHASE aminoadipoyl-cysteinyl-aminobutyrate-FE-... -

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Basic information

Entry
Database: PDB / ID: 1obn
TitleISOPENICILLIN N SYNTHASE aminoadipoyl-cysteinyl-aminobutyrate-FE-NO COMPLEX
ComponentsISOPENICILLIN N SYNTHETASE
KeywordsOXIDOREDUCTASE / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS
Function / homology
Function and homology information


isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol
Similarity search - Function
Isopenicillin N synthase signature 1. / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase ...Isopenicillin N synthase signature 1. / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-ASV / : / HYDROXYAMINE / Isopenicillin N synthase
Similarity search - Component
Biological speciesEMERICELLA NIDULANS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsLong, A.J. / Clifton, I.J. / Roach, P.L. / Baldwin, J.E. / Schofield, C.J. / Rutledge, P.J.
Citation
Journal: Biochem.J. / Year: 2003
Title: Structural Studies on the Reaction of Isopenicillin N Synthase with the Substrate Analogue Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-D-Alpha-Aminobutyrate.
Authors: Long, A.J. / Clifton, I.J. / Roach, P.L. / Baldwin, J.E. / Schofield, C.J. / Rutledge, P.J.
#1: Journal: Nature / Year: 1997
Title: Structure of Isopenicillin N Synthase Complexed with Substrate and the Mechanism of Penicillin Formation
Authors: Roach, P.L. / Clifton, I.J. / Hensgens, C.M. / Shibata, N. / Schofield, C.J. / Hajdu, J. / Baldwin, J.E.
History
DepositionJan 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 30, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0965
Polymers37,5641
Non-polymers5324
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.750, 71.350, 101.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ISOPENICILLIN N SYNTHETASE / ISOPENICILLIN N SYNTHASE


Mass: 37563.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-ASV / DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-D-VINYLGLYCINE


Mass: 347.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N3O6S
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-HOA / HYDROXYAMINE / Hydroxylamine


Mass: 33.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3NO
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.27 Å3/Da / Density % sol: 45.3 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop / Details: Roach, P.L., (1996) Eur. J. Biochem., 242, 736.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mlithium sulfate1reservoir
2100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.826
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826 Å / Relative weight: 1
ReflectionResolution: 1.29→19.3 Å / Num. obs: 76397 / % possible obs: 88.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13
Reflection shellResolution: 1.29→1.36 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.1 / % possible all: 78.7
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 19.55 Å / Num. obs: 73254 / Num. measured all: 244112 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 1.3 Å / % possible obs: 88.1 % / Num. unique obs: 9493 / Num. measured obs: 22973 / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1BLZ
Resolution: 1.3→58.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.177 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2914 4 %RANDOM
Rwork0.166 ---
obs0.167 70330 87.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.3→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 31 255 2931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212747
X-RAY DIFFRACTIONr_bond_other_d0.0010.022346
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.9443734
X-RAY DIFFRACTIONr_angle_other_deg0.90435490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7033328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60115455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023086
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02563
X-RAY DIFFRACTIONr_nbd_refined0.2260.3516
X-RAY DIFFRACTIONr_nbd_other0.1870.32247
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.5203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9341.51649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31422660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.08531098
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7474.51074
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 164
Rwork0.21 4322
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)
112.6523-16.2495-8.679425.550414.835710.4857-0.18930.0965-0.19910.0198-0.39261.0186-0.1472-0.64550.5820.10190.0182-0.04870.1686-0.01530.1407-4.045237.7885-10.3546
26.74741.6443-2.57324.5562-2.80169.8901-0.36710.2382-0.2894-0.44230.1284-0.27540.77720.12080.23870.1431-0.0230.02170.0942-0.01360.076210.969225.1165-20.9075
32.9581-1.5836-0.79873.89111.885.5483-0.07160.1673-0.0817-0.00820.01040.05990.1918-0.13830.06120.0618-0.0115-0.00980.09770.03040.03417.572533.9243-21.6491
41.8809-0.8141-0.90124.2625-0.6492.04660.04850.06370.1572-0.2514-0.02360.3025-0.126-0.1549-0.0250.06480.0107-0.03190.09360.01080.05153.338336.8112-12.3995
50.8592-0.25361.73031.3747-0.2955.61040.0042-0.0331-0.08950.0068-0.04690.04350.0784-0.01960.04270.0388-0.0088-0.00080.04720.00410.05135.388719.8622-0.1841
63.77892.00987.32652.51935.116318.96980.0702-0.2904-0.15840.2917-0.0170.11420.1852-0.5895-0.05320.10430.00530.00910.08970.01280.06776.922423.135716.2398
75.59520.880.41324.9490.38134.32780.040.0692-0.04390.0668-0.0221-0.1165-0.02270.1038-0.01790.04520.0147-0.00930.0881-0.01270.019416.602532.503819.8919
8-0.0497-0.2026-0.69281.3521-0.96986.252-0.0047-0.10760.1330.13720.0446-0.0953-0.30290.6433-0.03990.0635-0.0118-0.00460.1391-0.02920.087521.651934.425616.3748
97.1173-2.461-1.99681.53961.653.5158-0.0369-0.44340.16660.0420.0040.0546-0.2186-0.00170.03290.07890.0153-0.01550.0872-0.02050.06456.591937.074818.6986
103.7684-0.0872-2.01730.55930.34121.5715-0.011-0.2160.01880.02690.0159-0.09880.01880.1083-0.00480.03360.0104-0.01580.05350.00230.02721.661727.36686.3756
119.2762-4.98990.53458.5740.30172.4905-0.0252-0.27480.35230.00820.0867-0.4703-0.02960.0615-0.06150.038-0.0052-0.01810.0997-0.02120.07832.833932.62985.5295
124.67023.4508-1.96043.9398-1.27882.57340.1539-0.3659-0.16670.3302-0.2259-0.02330.12720.16760.0720.07560.0106-0.00460.09270.00710.054520.182523.039313.3361
130.9855-0.40950.68043.3445-2.6466.6475-0.0124-0.0456-0.14990.11460.00060.02450.24380.00920.01180.0546-0.00230.00410.03980.00250.048214.234318.52827.0598
140.9222-1.16131.48211.6384-1.61694.0562-0.00430.0771-0.0526-0.11320.0031-0.02280.12550.01390.00120.0329-0.00160.00320.04810.00190.028915.517125.9566-6.4434
152.20910.7445-1.29872.7763-1.36437.8833-0.0481-0.00590.0197-0.1125-0.0579-0.1984-0.06040.33130.1060.0561-0.0153-0.01350.0730.01790.045216.372535.6278-18.5437
161.5573-2.15872.80752.6768-3.96567.45180.03060.30.0654-0.2472-0.1224-0.2950.16380.33110.09180.0741-0.00550.00710.11920.01970.069423.425532.1206-12.5644
178.30840.1949-3.89751.07650.10063.31240.05570.03710.12460.0264-0.03680.0055-0.0747-0.0667-0.01890.02610.0074-0.02120.0356-0.00030.018312.952631.4195.275
180.81960.28050.253114.2799-0.18463.5329-0.0619-0.27930.21580.924-0.09320.1609-0.4234-0.26410.15510.15220.0095-0.02820.1411-0.01820.1086-4.201138.351518.0777
195.0535-3.1032-0.475210.9669-0.61923.6857-0.0085-0.23180.2950.4087-0.05190.0729-0.27430.04830.06040.0942-0.00220.01650.08-0.01540.0977-2.020447.66898.3667
202.0069-0.5662-1.04791.04591.04372.17130.0723-0.04820.237-0.0270.0186-0.0241-0.20160.0199-0.09090.05010.0042-0.00220.06280.00080.053710.833341.9729-1.8546
212.2186-1.2437-0.39051.06240.12420.0924-0.0174-0.0685-0.07670.0995-0.06510.21080.0231-0.17440.08250.0706-0.0004-0.00790.1084-0.01380.0663-0.772534.92960.4249
225.15524.7681-1.133919.43780.5192.6901-0.0690.23070.4971-0.8183-0.05350.9434-0.2011-0.23090.12250.11240.0474-0.04380.13510.010.1221-3.327144.8556-5.1634
233.23381.8203-0.00974.25920.49771.0068-0.0060.03550.107-0.0298-0.00080.27190.0616-0.07290.00680.04410.0099-0.01540.0655-0.00070.03854.877933.1668-5.8588
244.95690.45342.22011.78950.50875.50690.08710.14180.399-0.2266-0.0547-0.0208-0.2851-0.0998-0.03240.11330.00260.02210.07090.03240.0815.216846.018-12.4161
253.15741.4826-2.84081.2338-2.10843.80550.06470.12840.09020.03680.00880.0801-0.1285-0.2023-0.07340.06120.01020.00150.0676-0.01710.0737-0.463142.25663.6421
264.97430.7635-3.34480.8102-0.56882.94940.01120.05490.06090.0039-0.02750.0634-0.042-0.12140.01630.03220.0055-0.01810.0511-0.00270.03549.447832.26411.8898
272.8206-4.20265.34665.7871-8.576214.54880.15770.25710.1852-0.2491-0.2106-0.1431-0.1870.47240.05290.1239-0.00680.00950.1120.01030.120424.595242.9694-11.8062
282.75672.57413.70190.91111.727710.1917-0.2520.39540.244-0.41070.0653-0.0934-0.52290.36290.18670.27070.00710.03450.17420.02020.201820.858851.9585-18.6249
297.1691-2.2575-4.08464.8557-0.30979.6420.0568-0.39810.53860.35620.0477-0.3386-0.22750.4803-0.10450.0873-0.0122-0.01580.0771-0.00440.126823.083443.4957-0.449
307.6154-3.0672-4.03554.2162-1.27513.9849-0.0349-0.1088-0.1937-0.04950.16730.1624-0.07170.2329-0.13240.2045-0.0128-0.03450.1866-0.05240.202513.56345.90849.27
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 13
2X-RAY DIFFRACTION2A14 - 24
3X-RAY DIFFRACTION3A25 - 35
4X-RAY DIFFRACTION4A36 - 46
5X-RAY DIFFRACTION5A47 - 57
6X-RAY DIFFRACTION6A58 - 68
7X-RAY DIFFRACTION7A69 - 79
8X-RAY DIFFRACTION8A80 - 90
9X-RAY DIFFRACTION9A91 - 101
10X-RAY DIFFRACTION10A102 - 112
11X-RAY DIFFRACTION11A113 - 123
12X-RAY DIFFRACTION12A124 - 134
13X-RAY DIFFRACTION13A135 - 145
14X-RAY DIFFRACTION14A146 - 156
15X-RAY DIFFRACTION15A157 - 167
16X-RAY DIFFRACTION16A168 - 178
17X-RAY DIFFRACTION17A179 - 189
18X-RAY DIFFRACTION18A190 - 200
19X-RAY DIFFRACTION19A201 - 211
20X-RAY DIFFRACTION20A212 - 222
21X-RAY DIFFRACTION21A223 - 233
22X-RAY DIFFRACTION22A234 - 244
23X-RAY DIFFRACTION23A245 - 255
24X-RAY DIFFRACTION24A256 - 266
25X-RAY DIFFRACTION25A267 - 277
26X-RAY DIFFRACTION26A278 - 288
27X-RAY DIFFRACTION27A289 - 299
28X-RAY DIFFRACTION28A300 - 310
29X-RAY DIFFRACTION29A311 - 321
30X-RAY DIFFRACTION30A322 - 331
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

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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

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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

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