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- PDB-6qgb: Crystal structure of Ideonella sakaiensis MHETase bound to benzoi... -

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Basic information

Entry
Database: PDB / ID: 6qgb
TitleCrystal structure of Ideonella sakaiensis MHETase bound to benzoic acid
ComponentsMono(2-hydroxyethyl) terephthalate hydrolase
KeywordsHYDROLASE / Plastic-degrading hydrolase / alpha/beta hydrolase fold / I. sakaiensis catalytic triad
Function / homology
Function and homology information


mono(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / cell outer membrane / metal ion binding
Similarity search - Function
Tannase/feruloyl esterase / Tannase and feruloyl esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
BENZOIC ACID / Mono(2-hydroxyethyl) terephthalate hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsPalm, G.J. / Reisky, L. / Boettcher, D. / Mueller, H. / Michels, E.A.P. / Walczak, C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate.
Authors: Palm, G.J. / Reisky, L. / Bottcher, D. / Muller, H. / Michels, E.A.P. / Walczak, M.C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mono(2-hydroxyethyl) terephthalate hydrolase
B: Mono(2-hydroxyethyl) terephthalate hydrolase
C: Mono(2-hydroxyethyl) terephthalate hydrolase
D: Mono(2-hydroxyethyl) terephthalate hydrolase
E: Mono(2-hydroxyethyl) terephthalate hydrolase
F: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,40037
Polymers377,0656
Non-polymers2,33631
Water35,7421984
1
A: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2697
Polymers62,8441
Non-polymers4256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4488
Polymers62,8441
Non-polymers6047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1385
Polymers62,8441
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1385
Polymers62,8441
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1385
Polymers62,8441
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2697
Polymers62,8441
Non-polymers4256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.141, 184.048, 247.441
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, 6 molecules ABCDEF

#1: Protein
Mono(2-hydroxyethyl) terephthalate hydrolase / MHETase


Mass: 62844.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_0224
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0K8P8E7, mono(ethylene terephthalate) hydrolase

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Non-polymers , 6 types, 2015 molecules

#2: Chemical
ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1984 / 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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 30% (v/v) 2,4-MPD and 0.12 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 254053 / % possible obs: 98.9 % / Redundancy: 4.6 % / Net I/σ(I): 6.54
Reflection shellResolution: 2.2→2.33 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.2→46.086 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.11
RfactorNum. reflection% reflection
Rfree0.2135 2667 1.05 %
Rwork0.1854 --
obs0.1857 254007 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24717 0 125 1984 26826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725490
X-RAY DIFFRACTIONf_angle_d0.70734727
X-RAY DIFFRACTIONf_dihedral_angle_d12.75414906
X-RAY DIFFRACTIONf_chiral_restr0.0483638
X-RAY DIFFRACTIONf_plane_restr0.0054635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.199-2.2390.34561330.295412502X-RAY DIFFRACTION94
2.239-2.28210.29291400.279113211X-RAY DIFFRACTION100
2.2821-2.32860.30951400.278613216X-RAY DIFFRACTION100
2.3286-2.37930.32751400.26713181X-RAY DIFFRACTION99
2.3793-2.43460.29171390.262713135X-RAY DIFFRACTION99
2.4346-2.49550.29241390.256213091X-RAY DIFFRACTION99
2.4955-2.5630.23111410.239213244X-RAY DIFFRACTION100
2.563-2.63840.26761400.229213246X-RAY DIFFRACTION100
2.6384-2.72350.21061410.225913268X-RAY DIFFRACTION100
2.7235-2.82080.24161410.206813261X-RAY DIFFRACTION100
2.8208-2.93380.25531410.20513289X-RAY DIFFRACTION100
2.9338-3.06730.23491410.193413317X-RAY DIFFRACTION100
3.0673-3.22890.21591410.190813272X-RAY DIFFRACTION100
3.2289-3.43120.20431410.176613312X-RAY DIFFRACTION99
3.4312-3.6960.20951390.158913115X-RAY DIFFRACTION98
3.696-4.06770.16811420.141113355X-RAY DIFFRACTION100
4.0677-4.65590.14771420.125513387X-RAY DIFFRACTION99
4.6559-5.8640.17171430.141513426X-RAY DIFFRACTION99
5.864-46.09650.1531430.150713512X-RAY DIFFRACTION97
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)
12.90491.3780.12652.54941.07521.4558-0.1670.26320.5124-0.2748-0.03210.4705-0.6781-0.38740.2090.50370.1159-0.12110.41830.04420.46674.28659.3285-74.6832
22.08141.57940.43281.26370.05410.7088-0.1022-0.06510.1998-0.1295-0.06910.29-0.1455-0.10140.16350.32580.0673-0.02540.3273-0.02860.42393.43814.3982-62.0466
30.79710.23420.31041.2632-0.2691.1955-0.0734-0.03190.11270.0058-0.08250.1169-0.0782-0.05150.14530.30240.0221-0.0280.2916-0.03040.33119.94220.5149-61.5993
42.78211.8913-0.59322.3056-0.80221.202-0.0304-0.05770.121-0.12840.04720.2851-0.05-0.1914-0.07210.2930.0666-0.03340.3279-0.04740.3498-0.1255-6.9112-64.3219
51.19120.39790.06851.1386-0.3080.88810.0591-0.1474-0.1222-0.032-0.11560.04030.03880.00330.0470.26460.0138-0.00910.3294-0.01460.34810.3156-15.1763-57.8853
62.04540.112-0.26670.69540.27091.34060.2222-0.5643-0.28950.3307-0.2004-0.04390.15-0.2639-0.02180.4559-0.0782-0.07520.54480.10180.391418.9849-20.6029-32.6721
71.5715-0.1331-0.381.3404-0.3211.80330.2526-0.7221-0.4290.3823-0.1445-0.14540.0332-0.1341-0.15070.446-0.1361-0.04920.59750.14770.449513.766-26.5073-32.8331
85.03281.4764-0.03991.4296-0.70370.84220.2781-0.91050.34660.3573-0.25810.0432-0.139-0.3182-0.02420.4579-0.05330.01040.6199-0.02870.36229.6022-11.2681-34.1541
91.4355-0.10150.48422.14720.18452.31710.0638-0.5666-0.12820.3106-0.06270.18790.2213-0.47050.00810.3347-0.06010.00830.58390.00190.3992-5.8796-20.919-45.7888
101.12530.15340.58330.65480.11140.89750.1051-0.0522-0.19730.0357-0.0593-0.06910.1171-0.1026-0.05550.30450.0055-0.01020.29850.00350.376313.683-21.2255-59.8694
110.8872-0.08110.59031.11610.49313.53220.037-0.0832-0.02660.0006-0.0042-0.148-0.08560.2056-0.0240.2971-0.0013-0.01470.30590.01920.344325.8771-9.3565-55.7502
121.54360.18780.52650.71940.71331.58310.0042-0.1166-0.01340.15590.0384-0.29410.12920.2811-0.04640.36620.0146-0.04260.3840.05660.380634.2574-13.2039-45.4426
134.4794-1.73234.3771.2345-2.37875.3999-0.3377-0.7219-0.02090.3910.27350.1502-0.1484-0.53650.06640.44540.0480.06050.4592-0.00960.3333-27.7898-20.20531.3507
140.5071-0.09170.21190.33260.18690.98740.01310.0406-0.08510.03270.02360.01650.14430.0285-0.03140.2823-0.0134-0.00270.25050.00550.3133-21.2852-32.77981.9673
151.09320.01890.32190.80270.18420.96330.04750.0661-0.08470.0332-0.0094-0.03480.1480.0939-0.04040.2940.004100.29680.00150.2794-16.3314-31.4918-2.5589
166.1711-0.4075-4.98750.91121.57066.2153-0.1934-0.7369-0.09040.42150.0861-0.2312-0.02550.41180.09760.46150.0851-0.07860.38790.00380.3229-22.72411.906431.1156
170.6575-0.0949-0.08370.616-0.00990.7786-0.01370.03960.0576-0.00390.0172-0.0131-0.12140.0118-0.00920.3163-0.00710.00310.26690.00440.3242-27.743211.8715.6069
180.9980.0389-0.16641.0335-0.25850.8259-0.00420.19310.149-0.1759-0.0066-0.057-0.1752-0.00670.01120.4033-0.01570.01460.3420.01740.3238-26.472614.216-8.8786
191.3487-0.32870.11872.36590.05951.51010.03330.1820.1496-0.1657-0.06250.3197-0.238-0.25040.01490.34240.0333-0.01330.37270.01070.3581-48.376114.21230.866
202.87551.5371-0.31952.9815-0.74040.9755-0.24290.198-0.4194-0.24980.0856-0.42530.4630.13950.15710.48460.05270.09880.3876-0.03490.470446.51176.2237-75.8541
210.84280.3933-0.10040.6950.14260.8105-0.0422-0.0476-0.15550.0129-0.0241-0.14550.13390.14780.05570.32680.03320.0050.3330.03430.349444.592312.4632-61.4249
223.02191.59580.32471.94210.86791.6105-0.13460.0971-0.0313-0.23780.1056-0.1581-0.09460.17060.02990.2930.03560.0230.32610.05080.313248.154520.6044-67.1556
230.85270.1126-0.36430.42840.07090.5783-0.0032-0.23430.010.135-0.0019-0.0086-0.02420.2033-0.00020.33340.0143-0.02310.36930.01620.318537.754430.2321-41.4609
242.18790.3583-0.36571.7769-0.05572.2130.0402-0.4858-0.01020.2546-0.0173-0.05540.1180.2992-0.02910.3817-0.0098-0.05960.46590.00320.328840.723330.5942-31.036
251.46460.1632-0.27160.5925-0.18730.79560.0257-0.13850.0890.0386-0.0238-0.1092-0.05080.23080.00240.3026-0.0113-0.01880.33530.00050.339745.57434.0293-52.1626
260.97170.3629-1.35111.6355-0.70432.4709-0.0461-0.0269-0.10060.10270.03550.08810.0386-0.12-0.00740.30440.0139-0.01010.28260.01190.320525.375521.0728-50.1404
274.74292.9219-2.72794.7818-3.78633.85270.0393-0.09040.0466-0.14490.06360.54990.0209-0.1311-0.1050.33440.0047-0.02560.3354-0.03970.370816.03128.0449-45.1675
283.2843-1.03422.53041.6386-1.04054.3048-0.13720.39110.4323-0.25210.0728-0.1265-0.49390.43340.11150.4553-0.0870.00040.32380.02820.393415.1995-19.128229.1761
291.2231-0.07330.66430.75220.20440.4818-0.07520.1820.0802-0.13460.02350.0118-0.10540.1080.04610.3275-0.02650.01730.30570.00780.305611.5898-33.011228.9892
302.146-1.48410.77311.6013-0.11591.04440.00230.03610.0812-0.14850.0148-0.1698-0.03060.0258-0.01690.287-0.04290.03250.26460.00520.286616.5424-36.433835.1374
310.8508-0.0679-0.02380.65140.09110.4059-0.0412-0.0454-0.1363-0.02730.0533-0.01480.1008-0.0097-0.00930.3211-0.02340.01020.30280.02350.29567.9335-58.852839.9449
320.22220.57840.26082.63441.01460.7309-0.05330.0113-0.0388-0.07380.01690.2930.0104-0.10720.06490.3045-0.0281-0.01050.35490.03130.3343-6.7438-44.814634.928
332.68660.18180.88481.58871.77044.69370.00310.0328-0.06120.0014-0.04090.23040.2531-0.85870.03420.335-0.052-0.00790.36620.04440.3905-14.9184-55.798233.0031
342.8281-1.27741.50991.9875-0.79813.0923-0.21390.35220.452-0.42310.1334-0.1141-0.39150.28260.12310.495-0.1024-0.03520.34590.05860.43089.5135-0.9529-95.2149
352.0877-0.16531.72011.2760.02741.1856-0.07130.29640.0253-0.1518-0.0026-0.106-0.19250.21160.06310.3648-0.00870.04010.38430.02880.327110.5083-14.1229-98.5583
361.49110.16090.13221.1618-0.25540.6562-0.16220.14060.0459-0.14190.1118-0.0124-0.01340.06650.04030.3699-0.02-0.01610.3177-0.00830.29785.1494-17.7337-95.8784
372.1033-0.72590.64971.2154-0.39340.4746-0.2114-0.0580.11280.10420.0692-0.0707-0.09360.04860.14650.3284-0.0287-0.0250.306-0.04290.346910.6175-15.6682-86.9119
380.61590.5112-0.01260.7210.47290.7197-0.0734-0.0346-0.0755-0.04930.0756-0.0618-0.02790.09570.00820.28890.01990.00420.29270.00280.3133.8493-31.1141-85.3298
391.7182-0.1913-0.09080.5914-0.0120.4904-0.0390.1282-0.3237-0.1090.0557-0.06820.1394-0.0109-0.02270.3845-0.01470.03740.2922-0.02730.3957-3.0981-53.9146-93.9209
405.02930.20091.92261.4856-0.13861.2121-0.09380.5321-0.1259-0.38610.1211-0.14020.02320.2018-0.04050.4569-0.03920.06060.3715-0.06420.36134.0788-45.6888-102.5013
411.15750.50670.13491.2421-0.13031.5363-0.06440.0048-0.27560.01280.0975-0.26140.18810.2132-0.02260.33370.05040.00150.363-0.05560.481819.5974-42.4204-88.1076
421.07210.07610.26531.27220.48440.7544-0.0466-0.1024-0.04690.01070.0326-0.06790.0320.04390.00620.30780.02030.00010.30380.00860.2870.1436-31.062-79.2126
430.92551.11450.56481.68311.40792.5319-0.01730.05760.0511-0.118-0.12110.2063-0.0653-0.29850.12880.34370.0071-0.00520.29750.02130.3147-12.2466-27.2057-91.5028
443.2538-0.1381.49812.15871.18233.210.0096-0.0891-0.1609-0.18010.01540.3923-0.031-0.7256-0.02920.3486-0.0342-0.02210.3240.03750.3706-20.6677-37.7254-94.5025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 271 )
6X-RAY DIFFRACTION6chain 'A' and (resid 272 through 333 )
7X-RAY DIFFRACTION7chain 'A' and (resid 334 through 382 )
8X-RAY DIFFRACTION8chain 'A' and (resid 383 through 414 )
9X-RAY DIFFRACTION9chain 'A' and (resid 415 through 453 )
10X-RAY DIFFRACTION10chain 'A' and (resid 454 through 523 )
11X-RAY DIFFRACTION11chain 'A' and (resid 524 through 560 )
12X-RAY DIFFRACTION12chain 'A' and (resid 561 through 603 )
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 76 )
14X-RAY DIFFRACTION14chain 'B' and (resid 77 through 382 )
15X-RAY DIFFRACTION15chain 'B' and (resid 383 through 603 )
16X-RAY DIFFRACTION16chain 'C' and (resid 43 through 76 )
17X-RAY DIFFRACTION17chain 'C' and (resid 77 through 333 )
18X-RAY DIFFRACTION18chain 'C' and (resid 334 through 523 )
19X-RAY DIFFRACTION19chain 'C' and (resid 524 through 603 )
20X-RAY DIFFRACTION20chain 'D' and (resid 43 through 76 )
21X-RAY DIFFRACTION21chain 'D' and (resid 77 through 177 )
22X-RAY DIFFRACTION22chain 'D' and (resid 178 through 217 )
23X-RAY DIFFRACTION23chain 'D' and (resid 218 through 333 )
24X-RAY DIFFRACTION24chain 'D' and (resid 334 through 414 )
25X-RAY DIFFRACTION25chain 'D' and (resid 415 through 523 )
26X-RAY DIFFRACTION26chain 'D' and (resid 524 through 572 )
27X-RAY DIFFRACTION27chain 'D' and (resid 573 through 603 )
28X-RAY DIFFRACTION28chain 'E' and (resid 43 through 76 )
29X-RAY DIFFRACTION29chain 'E' and (resid 77 through 148 )
30X-RAY DIFFRACTION30chain 'E' and (resid 149 through 212 )
31X-RAY DIFFRACTION31chain 'E' and (resid 213 through 523 )
32X-RAY DIFFRACTION32chain 'E' and (resid 524 through 560 )
33X-RAY DIFFRACTION33chain 'E' and (resid 561 through 603 )
34X-RAY DIFFRACTION34chain 'F' and (resid 43 through 76 )
35X-RAY DIFFRACTION35chain 'F' and (resid 77 through 110 )
36X-RAY DIFFRACTION36chain 'F' and (resid 111 through 177 )
37X-RAY DIFFRACTION37chain 'F' and (resid 178 through 217 )
38X-RAY DIFFRACTION38chain 'F' and (resid 218 through 271 )
39X-RAY DIFFRACTION39chain 'F' and (resid 272 through 382 )
40X-RAY DIFFRACTION40chain 'F' and (resid 383 through 414 )
41X-RAY DIFFRACTION41chain 'F' and (resid 415 through 452 )
42X-RAY DIFFRACTION42chain 'F' and (resid 453 through 523 )
43X-RAY DIFFRACTION43chain 'F' and (resid 524 through 560 )
44X-RAY DIFFRACTION44chain 'F' and (resid 561 through 603 )

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