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- PDB-4h9x: Structure of Geobacillus kaustophilus lactonase, mutant E101G/R23... -

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Basic information

Entry
Database: PDB / ID: 4h9x
TitleStructure of Geobacillus kaustophilus lactonase, mutant E101G/R230C/D266N with Zn2+ and bound N-butyryl-DL-homoserine lactone
ComponentsPhosphotriesterase
KeywordsHYDROLASE / (beta/alpha)8 barrel
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / catabolic process / hydrolase activity / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / HYDROXIDE ION / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.201 Å
AuthorsXue, B. / Chow, J.Y. / Yew, W.S. / Robinson, R.C.
CitationJournal: Biochemistry / Year: 2013
Title: Structural evidence of a productive active site architecture for an evolved quorum-quenching GKL lactonase.
Authors: Xue, B. / Chow, J.Y. / Baldansuren, A. / Yap, L.L. / Gan, Y.H. / Dikanov, S.A. / Robinson, R.C. / Yew, W.S.
History
DepositionSep 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,12510
Polymers73,5062
Non-polymers6198
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-132 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.552, 129.156, 51.637
Angle α, β, γ (deg.)90.000, 95.840, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 3:99 or resseq 108:144 or resseq...A0
211chain 'B' and (resseq 3:99 or resseq 108:144 or resseq...B0

NCS oper: (Code: given
Matrix: (0.10225, -0.000937, -0.994758), (0.000223, -1, 0.000965), (-0.994759, -0.000321, -0.10225)
Vector: -0.013806, 70.208504, -0.025828)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphotriesterase


Mass: 36752.828 Da / Num. of mol.: 2 / Mutation: E101G,R230C,D266N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1506 / Plasmid: pET-15b, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds

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Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Chemical ChemComp-HL4 / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / N-butyryl-L-homoserine lactone


Mass: 171.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: sitting-drop vapor diffusion / pH: 7.5
Details: 100 mM Tris, pH 7.5, 20% (w/v) PEG 4000, 10% (v/v) glycerol, 0.1 mM ZnCl2, 1.0mM N-butyryl-DL-homoserine lactone, sitting-drop vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33918 / Num. obs: 33918 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.03 / Χ2: 0.836 / Net I/σ(I): 18.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.242.90.27314780.938183.7
2.24-2.283.20.2516261.002199.4
2.28-2.323.40.24317451.01199.7
2.32-2.373.60.20316920.979199.9
2.37-2.423.70.18316890.935199.9
2.42-2.483.70.15217350.961100
2.48-2.543.80.13416790.9681100
2.54-2.613.70.1117120.915199.8
2.61-2.693.80.08717190.868199.9
2.69-2.773.80.07317030.8621100
2.77-2.873.80.05717300.826199.9
2.87-2.993.80.04616710.795199.8
2.99-3.123.80.03517050.712199.9
3.12-3.293.80.02717240.663199.9
3.29-3.493.80.02417190.657199.8
3.49-3.763.80.02117080.646199.8
3.76-4.143.70.02317100.8771100
4.14-4.743.70.02317381.119199.9
4.74-5.973.60.01917010.649199.4
5.97-503.70.01517340.435198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.85 Å
Translation3.5 Å19.85 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→19.853 Å / Occupancy max: 1 / Occupancy min: 0.65 / SU ML: 0.23 / σ(F): 0 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 1645 5.08 %random
Rwork0.1763 ---
obs0.1783 32403 95.4 %-
all-32403 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.118 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 142.77 Å2 / Biso mean: 38.175 Å2 / Biso min: 4.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.9515 Å20 Å21.2053 Å2
2--1.3344 Å20 Å2
3---0.1235 Å2
Refinement stepCycle: LAST / Resolution: 2.201→19.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 30 189 5233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095154
X-RAY DIFFRACTIONf_angle_d1.1746970
X-RAY DIFFRACTIONf_chiral_restr0.08754
X-RAY DIFFRACTIONf_plane_restr0.006912
X-RAY DIFFRACTIONf_dihedral_angle_d15.5431906
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2328X-RAY DIFFRACTIONPOSITIONAL0.019
12B2328X-RAY DIFFRACTIONPOSITIONAL0.019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2014-2.26610.3174760.2241625170160
2.2661-2.33910.25481370.23332314245188
2.3391-2.42260.3031400.21672627276799
2.4226-2.51940.2381380.198327042842100
2.5194-2.63380.20721540.184626832837100
2.6338-2.77230.24751450.186226692814100
2.7723-2.94550.25271450.191526822827100
2.9455-3.1720.23251500.187426692819100
3.172-3.48970.22191370.185526972834100
3.4897-3.99110.19321420.167526962838100
3.9911-5.01490.16611390.135526882827100
5.0149-19.85410.18661420.16082704284699
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)
10.0023-0.00280.00380.0055-0.00090.0074-0.0097-0.0156-0.00430.0167-0.0076-0.01340.00240.0142-0.03230.07530.0586-0.03670.26010.17430.016216.591525.812122.0843
20.0410.0415-0.02340.0387-0.0180.0631-0.0598-0.0589-0.05510.0296-0.0384-0.02220.02860.0384-0.20050.15070.09670.005-0.01440.15710.11676.292724.787-0.7481
30.01930.01360.00870.01120.00360.0084-0.0020.0025-0.01290.0015-0.00050.00530.0113-0.0117-0.00170.2415-0.16160.05680.23570.02720.2661-4.389521.91214.5665
40.00050.0005-0.00070.00190.00150.0043-0.0037-0.01-0.01570.0165-0.0227-0.00010.03550-0.04630.3083-0.13150.07630.13180.21490.30735.289312.921312.175
50.05970.0467-0.07690.0346-0.05870.097-0.0487-0.0692-0.048-0.0357-0.0033-0.0018-0.0080.0343-0.09190.11910.05520.01530.0350.15560.023310.140825.93488.6432
60.02-0.01130.00010.0465-0.03450.0295-0.0001-0.0116-0.01170.00410.00280.0096-0.0007-0.00360.0110.2117-0.00260.14620.29050.09030.20641.663523.698816.7268
70.0454-0.0090.01610.01310.01540.0347-0.0074-0.0542-0.05490.04240.00580.01610.06200.00490.1001-0.01720.0620.13010.1120.063912.90831.43814.1521
80.00060.00080.00140.00080.00160.003-0.00590.0138-0.0076-0.0037-0.010.0003-0.00210.0057-0.00010.3202-0.00180.03570.2740.0480.299415.934747.7391-7.2602
90.04530.0017-0.00670.0129-0.00140.001-0.0029-0.0510.03980.01060.0064-0.0176-0.03430.01960.01190.0736-0.0396-0.00340.0996-0.04330.093617.390844.16875.7748
100.0049-0.00620.00760.0063-0.00890.00970.0059-0.0217-0.0061-0.00310.00960.0124-0.0074-0.03710.0395-0.00780.03060.01310.15510.0062-0.0313.83934.44658.9251
110.0005-0.0017-0.00060.0110.00590.00470.00590.00880.0147-0.004-0.00280.000800.005400.17170.06580.06280.21320.00930.155326.655733.4861-9.812
120.00980.00710.0130.02570.01030.0221-0.0328-0.01260.0514-0.0201-0.00460.0065-0.01490.0131-0.0209-0.0189-0.048-0.04890.2159-0.03390.097724.351438.51884.8686
130.03930.03020.0110.02440.00710.04180.006-0.0418-0.069-0.0296-0.0108-0.00030.04280.0447-0.0518-0.0290.1525-0.06190.19710.08560.094530.248526.02150.4874
140.0172-0.0324-0.00350.06140.01860.0203-0.02290.0015-0.0375-0.0162-0.03360.0220.04250.0449-0.15690.08850.17390.00830.17970.1640.237626.354618.48540.0234
150.00190.0034-0.00290.0111-0.0080.0061-0.00310.0049-0.0097-0.0014-0.0045-0.01310.01010.0027-0.00110.40240.18220.07150.21360.00660.515426.99218.1274-2.8574
160.0436-0.02560.02270.0147-0.01250.01280.0166-0.0008-0.02670.01070.0036-0.00270.00250.01040.01520.23820.2588-0.0910.31290.19510.378234.061613.5298.0598
170.0364-0.0131-0.00950.01860.00620.0019-0.03850.0145-0.06120.0114-0.0405-0.0370.02710.0286-0.12970.1753-0.04530.0405-0.03180.05190.22448.08116.0992-4.3003
180.0063-0.0068-0.00230.0173-0.00030.00220.0023-0.0021-0.027-0.0186-0.0210.02790.00860.0088-0.02890.39740.02170.05320.06830.0950.562216.14876.88092.5007
190.0011-0.00130.00110.00290.00290.0093-0.0105-0.0016-0.01070.0014-0.0212-0.00610.00590.0007-00.58960.2095-0.10890.42050.15120.604629.92892.783212.9796
200.0042-0.00710.00390.0138-0.00930.0052-0.0096-0.0175-0.0220.0075-0.0101-0.01610.03140.0219-0.03220.19190.1162-0.01110.33150.29220.221626.134217.730116.3345
210.0112-0.0065-0.00310.01590.00310.00030.00930.00360.0028-0.0142-0.00420.0301-0.0034-0.0148-0.00220.02610.1363-0.05840.28830.09160.0931-20.30444.3726-18.8243
220.0366-0.00440.00020.01110.01930.02770.04970.020.0286-0.0129-0.0010.0134-0.0465-0.04930.06780.08780.16540.0061-0.0720.10330.11451.352845.4114-6.2427
230.00310.00640.00610.0170.00520.0230.0072-0.01230.00940.00680.00210.0082-0.01470.00160.00540.29250.06110.05220.2405-0.16050.2468-5.027848.3023.8354
240.0039-0.002-0.00070.0033-0.00220.00440.0048-0.01030.0183-0.0008-0.00530.0145-0.0183-0.0037-0.00430.32460.22380.06420.1423-0.10740.3618-11.60757.282-6.5787
250.0983-0.0481-0.07030.04690.03240.05130.02710.02210.00420.00840.0098-0.0124-0.0561-0.08280.08690.00050.172-0.04030.00890.06440.0808-7.59244.2605-11.0287
260.0235-0.02180.00560.0253-0.01320.01320-0.0056-0.00010.00940.00090.0056-0.0127-0.0103-0.00010.14430.0770.12380.24640.00090.1738-16.505146.5017-3.4278
270.03430.0020.02170.0246-0.01960.0404-0.0010.00940.09610.003-0.00150.0398-0.0701-0.0545-0.00570.07330.10060.02990.10820.01150.1202-2.837338.7532-13.3252
280.00850.0018-0.00340.0007-0.00160.00460.00770.0013-0.00580.0034-0.0026-0.0054-0.00260.013100.28030.03650.05790.2813-0.0160.34788.821622.4552-15.1445
290.00020.0001-0.00010.0109-0.01350.0264-0.00780.0249-0.0323-0.0333-0.0010.00110.0255-0.045-0.01040.1059-0.0358-0.00250.0989-0.060.0805-3.997226.0245-17.9329
300.0088-0.00950.00520.0098-0.00820.0075-0.0088-0.0358-0.0080.0108-0.00860.0044-0.0046-0.0395-0.0441-0.01520.01420.02550.1880.02510.0077-7.497735.747-14.7291
310.00410.00490.00120.01080.00160.0014-0.02020.0064-0.00720.0028-0.0158-0.00230.02410.0049-0.00010.11830.00940.07310.21520.05920.200112.453536.7002-25.5614
320.01050.00380.00960.01060.00230.01150.01180.0167-0.00170.00060.0019-0.01690.0361-0.019-0.0010.1046-0.0134-0.02340.2084-0.05-0.0357-2.38531.668-24.7681
330.0376-0.00390.00990.01420.01570.0268-0.00020.06120.0332-0.0029-0.0126-0.0241-0.0375-0.0227-0.01620.0980.0624-0.03830.20020.1782-0.03842.574644.1585-30.1981
340.0087-0.00230.00620.0177-0.01190.00910.01410.03690.05120.0276-0.0058-0.0088-0.0317-0.00410.08840.23790.15490.00890.19140.1920.11232.627651.705-26.3241
350.002-0.00140.0010.0112-0.00230.00160.00150.0040.0067-0.0155-0.0029-0.0038-0.00780.0034-0.00490.46680.0140.09110.21640.1910.38295.565962.0538-26.6353
360.0027-0.00430.00750.0088-0.01560.027-0.00630.0123-0.00080.0001-0.00120.0128-0.025-0.0005-0.00480.34360.17-0.05390.27350.28820.2132-4.576256.6439-34.7805
370.0011-0.0014-0.00920.0182-0.00510.04020.03020.01540.0397-0.0184-0.0082-0.0078-0.04920.01720.04120.230.0580.0455-0.0487-0.02020.23045.091354.116-7.6362
380.0026-0.00670.00510.0132-0.00980.0081-0.00210.00830.02310.0089-0.0175-0.0009-0.0327-0.0002-0.00510.46820.09180.06220.03220.0210.4119-0.881263.3402-16.4056
390.0008-0.00110.00060.0015-0.00110.00060.0141-0.00340.0071-0.0014-0.0004-0.0011-0.00730.0021-00.63180.1595-0.06230.39030.21510.5716-9.890667.3922-31.1823
400.0029-0.00580.00360.01-0.00660.00340.01250.01360.0293-0.0116-0.00070.0045-0.0133-0.01780.01470.20190.2382-0.01420.29630.12520.2067-13.612952.4498-27.7333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:19)A3 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:41)A20 - 41
3X-RAY DIFFRACTION3(chain A and resid 42:47)A42 - 47
4X-RAY DIFFRACTION4(chain A and resid 48:61)A48 - 61
5X-RAY DIFFRACTION5(chain A and resid 62:81)A62 - 81
6X-RAY DIFFRACTION6(chain A and resid 82:87)A82 - 87
7X-RAY DIFFRACTION7(chain A and resid 88:109)A88 - 109
8X-RAY DIFFRACTION8(chain A and resid 110:114)A110 - 114
9X-RAY DIFFRACTION9(chain A and resid 115:131)A115 - 131
10X-RAY DIFFRACTION10(chain A and resid 132:149)A132 - 149
11X-RAY DIFFRACTION11(chain A and resid 150:155)A150 - 155
12X-RAY DIFFRACTION12(chain A and resid 156:175)A156 - 175
13X-RAY DIFFRACTION13(chain A and resid 176:217)A176 - 217
14X-RAY DIFFRACTION14(chain A and resid 218:240)A218 - 240
15X-RAY DIFFRACTION15(chain A and resid 241:248)A241 - 248
16X-RAY DIFFRACTION16(chain A and resid 249:262)A249 - 262
17X-RAY DIFFRACTION17(chain A and resid 263:282)A263 - 282
18X-RAY DIFFRACTION18(chain A and resid 283:302)A283 - 302
19X-RAY DIFFRACTION19(chain A and resid 303:310)A303 - 310
20X-RAY DIFFRACTION20(chain A and resid 311:325)A311 - 325
21X-RAY DIFFRACTION21(chain B and resid 3:19)B3 - 19
22X-RAY DIFFRACTION22(chain B and resid 20:41)B20 - 41
23X-RAY DIFFRACTION23(chain B and resid 42:47)B42 - 47
24X-RAY DIFFRACTION24(chain B and resid 48:61)B48 - 61
25X-RAY DIFFRACTION25(chain B and resid 62:81)B62 - 81
26X-RAY DIFFRACTION26(chain B and resid 82:87)B82 - 87
27X-RAY DIFFRACTION27(chain B and resid 88:109)B88 - 109
28X-RAY DIFFRACTION28(chain B and resid 110:114)B110 - 114
29X-RAY DIFFRACTION29(chain B and resid 115:131)B115 - 131
30X-RAY DIFFRACTION30(chain B and resid 132:149)B132 - 149
31X-RAY DIFFRACTION31(chain B and resid 150:155)B150 - 155
32X-RAY DIFFRACTION32(chain B and resid 156:175)B156 - 175
33X-RAY DIFFRACTION33(chain B and resid 176:217)B176 - 217
34X-RAY DIFFRACTION34(chain B and resid 218:240)B218 - 240
35X-RAY DIFFRACTION35(chain B and resid 241:248)B241 - 248
36X-RAY DIFFRACTION36(chain B and resid 249:262)B249 - 262
37X-RAY DIFFRACTION37(chain B and resid 263:282)B263 - 282
38X-RAY DIFFRACTION38(chain B and resid 283:302)B283 - 302
39X-RAY DIFFRACTION39(chain B and resid 303:310)B303 - 310
40X-RAY DIFFRACTION40(chain B and resid 311:325)B311 - 325

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