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- PDB-7q05: Crystal structure of TPADO in complex with TPA -

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Basic information

Entry
Database: PDB / ID: 7q05
TitleCrystal structure of TPADO in complex with TPA
Components
  • (Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit ...) x 2
  • Lysozyme
KeywordsOXIDOREDUCTASE / terephthalic acid / TPA
Function / homology
Function and homology information


terephthalate 1,2-dioxygenase / terephthalate 1,2-dioxygenase activity / phthalate metabolic process / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 2 iron, 2 sulfur cluster binding / cell wall macromolecule catabolic process / lysozyme ...terephthalate 1,2-dioxygenase / terephthalate 1,2-dioxygenase activity / phthalate metabolic process / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 2 iron, 2 sulfur cluster binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / iron ion binding / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Ring-hydroxylating dioxygenase, large/alpha subunit AhdA1c-like, C-terminal / SnoaL-like domain / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / SnoaL-like domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain ...Ring-hydroxylating dioxygenase, large/alpha subunit AhdA1c-like, C-terminal / SnoaL-like domain / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / SnoaL-like domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / terephthalic acid / Lysozyme C / Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 / Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
Similarity search - Component
Biological speciesComamonas sp. (bacteria)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsZahn, M. / Kincannon, W.M. / DuBois, J.L. / McGeehan, J.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Biochemical and structural characterization of an aromatic ring-hydroxylating dioxygenase for terephthalic acid catabolism.
Authors: Kincannon, W.M. / Zahn, M. / Clare, R. / Lusty Beech, J. / Romberg, A. / Larson, J. / Bothner, B. / Beckham, G.T. / McGeehan, J.E. / DuBois, J.L.
History
DepositionOct 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
B: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
C: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
D: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
E: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
F: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
H: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,77426
Polymers210,5807
Non-polymers2,19419
Water17,168953
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26150 Å2
ΔGint-352 kcal/mol
Surface area62510 Å2
Unit cell
Length a, b, c (Å)219.714, 219.714, 82.964
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C
74D
84E
95D
105F
116E
126F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLEULEUAA1 - 1541 - 154
221METMETLEULEUBB1 - 1541 - 154
332METMETLEULEUAA1 - 1541 - 154
442METMETLEULEUCC1 - 1541 - 154
553METMETLEULEUBB1 - 1541 - 154
663METMETLEULEUCC1 - 1541 - 154
774GLUGLUGLUGLUDD3 - 4105 - 412
884GLUGLUGLUGLUEE3 - 4105 - 412
995SERSERMETMETDD4 - 4116 - 413
10105SERSERMETMETFF4 - 4116 - 413
11116SERSERGLNGLNEE4 - 4126 - 414
12126SERSERGLNGLNFF4 - 4126 - 414

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit ... , 2 types, 6 molecules ABCDEF

#1: Protein Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1 / / TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2- ...TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2-dioxygenase small subunit 1


Mass: 17249.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas sp. (bacteria) / Gene: tphA3I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3C1E2, terephthalate 1,2-dioxygenase
#2: Protein Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 / / TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2- ...TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2-dioxygenase large subunit 2


Mass: 48166.754 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas sp. (bacteria) / Gene: tphA2II / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3C1D5, terephthalate 1,2-dioxygenase

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Protein , 1 types, 1 molecules H

#3: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 972 molecules

#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-UB7 / terephthalic acid / benzene-1,4-dicarboxylic acid / Terephthalic acid


Mass: 166.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 953 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate, 0.1 M buffer Imidazole/MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.078→190.278 Å / Num. obs: 111025 / % possible obs: 96 % / Redundancy: 21.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.037 / Net I/σ(I): 14
Reflection shellResolution: 2.078→2.254 Å / Redundancy: 21.4 % / Rmerge(I) obs: 2.514 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5551 / CC1/2: 0.667 / Rpim(I) all: 0.557 / % possible all: 65.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N0Q, 3EBY
Resolution: 2.08→190.278 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.824 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.183
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.214 5502 4.956 %
Rwork0.1679 105521 -
all0.17 --
obs-111023 80.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.213 Å2
Baniso -1Baniso -2Baniso -3
1--0.038 Å2-0.019 Å2-0 Å2
2---0.038 Å20 Å2
3---0.122 Å2
Refinement stepCycle: LAST / Resolution: 2.08→190.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13875 0 105 953 14933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01314322
X-RAY DIFFRACTIONr_bond_other_d0.0020.01513082
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.63719384
X-RAY DIFFRACTIONr_angle_other_deg1.4161.58130050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78251770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13422.037820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.199152347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7815105
X-RAY DIFFRACTIONr_chiral_restr0.0830.21820
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216643
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023512
X-RAY DIFFRACTIONr_nbd_refined0.2010.22758
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.212748
X-RAY DIFFRACTIONr_nbtor_refined0.1690.26849
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.27083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2955
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0420.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.253
X-RAY DIFFRACTIONr_nbd_other0.2430.2137
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.219
X-RAY DIFFRACTIONr_mcbond_it2.1993.3557068
X-RAY DIFFRACTIONr_mcbond_other2.1983.3547067
X-RAY DIFFRACTIONr_mcangle_it3.1945.0248818
X-RAY DIFFRACTIONr_mcangle_other3.1945.0248819
X-RAY DIFFRACTIONr_scbond_it2.9883.6657254
X-RAY DIFFRACTIONr_scbond_other2.943.6577242
X-RAY DIFFRACTIONr_scangle_it4.265.3910552
X-RAY DIFFRACTIONr_scangle_other4.2015.37810534
X-RAY DIFFRACTIONr_lrange_it6.46639.74516075
X-RAY DIFFRACTIONr_lrange_other6.44339.30515834
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.054756
X-RAY DIFFRACTIONr_ncsr_local_group_20.0970.054739
X-RAY DIFFRACTIONr_ncsr_local_group_30.0860.054819
X-RAY DIFFRACTIONr_ncsr_local_group_40.1020.0512000
X-RAY DIFFRACTIONr_ncsr_local_group_50.0850.0512172
X-RAY DIFFRACTIONr_ncsr_local_group_60.10.0512117
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.088660.05009
12BX-RAY DIFFRACTIONLocal ncs0.088660.05009
23AX-RAY DIFFRACTIONLocal ncs0.096760.05009
24CX-RAY DIFFRACTIONLocal ncs0.096760.05009
35BX-RAY DIFFRACTIONLocal ncs0.085860.05009
36CX-RAY DIFFRACTIONLocal ncs0.085860.05009
47DX-RAY DIFFRACTIONLocal ncs0.10210.05008
48EX-RAY DIFFRACTIONLocal ncs0.10210.05008
59DX-RAY DIFFRACTIONLocal ncs0.085290.05009
510FX-RAY DIFFRACTIONLocal ncs0.085290.05009
611EX-RAY DIFFRACTIONLocal ncs0.100120.05008
612FX-RAY DIFFRACTIONLocal ncs0.100120.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.08-2.1340.3250.2543040.258101190.8260.8483.25130.243
2.134-2.1920.306740.25914890.26197900.8060.83815.96530.253
2.192-2.2560.2312200.23835730.23895750.880.8739.61360.228
2.256-2.3250.2774030.23367260.23592860.8530.87576.77150.219
2.325-2.4020.284290.23284580.23489760.8640.88399.00850.212
2.402-2.4860.2473930.21683440.21787370.8980.9061000.191
2.486-2.580.2523930.20680450.20884380.9050.9191000.178
2.58-2.6850.2594050.19176930.19480980.9070.9331000.164
2.685-2.8050.2523650.18274010.18577660.9210.9421000.156
2.805-2.9410.223820.17570590.17774410.9370.9471000.152
2.941-3.10.2293740.17567210.17870950.9380.9511000.156
3.1-3.2880.2143190.17263560.17466760.9420.95599.9850.158
3.288-3.5150.2153000.17660000.17763000.9480.9591000.165
3.515-3.7970.1913100.16755860.16958960.9570.9621000.159
3.797-4.1590.1812570.14451580.14554150.9650.9731000.139
4.159-4.650.1522540.11946570.12149110.9730.9791000.121
4.65-5.3690.1632080.12641370.12843450.9720.9791000.13
5.369-6.5740.2141870.16334980.16636850.9540.9651000.164
6.574-9.2910.2231230.15527650.15828880.9470.9631000.162
9.291-190.2780.329810.20115510.20716320.7840.9121000.22
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)
11.2407-0.6267-1.09992.76190.71071.47040.0640.1829-0.0482-0.108-0.15140.3242-0.0204-0.22170.08740.07060.033-0.0110.0462-0.01780.04-80.6562-41.42680.8831
21.97890.2888-0.22371.65620.64032.09340.0222-0.3458-0.0180.2431-0.0120.1271-0.0269-0.1062-0.01020.07920.02360.00360.07910.00610.0247-79.5637-63.579117.9509
31.6331-0.78060.10531.63510.72631.9574-0.0179-0.10640.1980.06850.0763-0.1167-0.3313-0.015-0.05840.10860.02920.01740.039-0.0030.0295-58.9904-44.423718.5083
40.77490.00320.19911.2699-0.07491.111-0.01630.25430.0411-0.29040.0160.0073-0.15830.02510.00020.25870.0320.0720.09230.02920.0347-61.6788-44.822-23.413
51.0282-0.02540.1011.3577-0.13690.71610.04-0.0323-0.1574-0.0536-0.00770.04480.0583-0.0283-0.03230.05080.0259-0.04370.0209-0.01780.0537-75.8004-84.0381-5.9211
61.18420.20610.22680.73090.02521.02210.02990.0390.0218-0.0616-0.0015-0.3001-0.1410.2118-0.02850.06820.01770.02790.1005-0.0130.1365-38.5611-65.2488.1235
72.0064-0.0915-0.61051.18280.21864.39970.0364-0.38650.16990.1042-0.0617-0.131-0.07140.41620.02530.0471-0.0125-0.02610.1057-0.03050.1207-74.0185-16.542329.0782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 154
2X-RAY DIFFRACTION2ALLB1 - 154
3X-RAY DIFFRACTION3ALLC1 - 154
4X-RAY DIFFRACTION4ALLD3 - 411
5X-RAY DIFFRACTION4ALLD501
6X-RAY DIFFRACTION4ALLD502
7X-RAY DIFFRACTION4ALLD503
8X-RAY DIFFRACTION5ALLE3 - 426
9X-RAY DIFFRACTION5ALLE501
10X-RAY DIFFRACTION5ALLE502
11X-RAY DIFFRACTION5ALLE503
12X-RAY DIFFRACTION5ALLE504
13X-RAY DIFFRACTION5ALLE505
14X-RAY DIFFRACTION6ALLF4 - 413
15X-RAY DIFFRACTION6ALLF501
16X-RAY DIFFRACTION6ALLF502
17X-RAY DIFFRACTION6ALLF503
18X-RAY DIFFRACTION7ALLH1 - 129
19X-RAY DIFFRACTION7ALLH201

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