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- PDB-5hss: Linalool dehydratase/isomerase: Ldi with monoterpene substrate -

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Basic information

Entry
Database: PDB / ID: 5hss
TitleLinalool dehydratase/isomerase: Ldi with monoterpene substrate
ComponentsLinalool dehydratase/isomerase
KeywordsLYASE / Linalool dehydratase/isomerase / alpha6 alpha6 barrel fold / myrcene / geraniol
Function / homology
Function and homology information


linalool dehydratase / geraniol isomerase / monoterpene catabolic process / intramolecular hydroxytransferase activity / monoterpenoid metabolic process / hydro-lyase activity / cellular response to organic substance / protein tetramerization / periplasmic space
Similarity search - Function
Linalool dehydratase/isomerase / Linalool dehydratase/isomerase
Similarity search - Domain/homology
Geraniol / Beta-Myrcene / Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCastellaniella defragrans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsWeidenweber, S. / Marmulla, R. / Harder, J. / Ermler, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
DFG (Sina Weidenweber)SPP1319 Germany
CitationJournal: Febs Lett. / Year: 2016
Title: X-ray structure of linalool dehydratase/isomerase from Castellaniella defragrans reveals enzymatic alkene synthesis.
Authors: Weidenweber, S. / Marmulla, R. / Ermler, U. / Harder, J.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Linalool dehydratase/isomerase
B: Linalool dehydratase/isomerase
C: Linalool dehydratase/isomerase
D: Linalool dehydratase/isomerase
E: Linalool dehydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,65315
Polymers209,3135
Non-polymers1,34010
Water2,180121
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-40 kcal/mol
Surface area61360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.270, 106.290, 221.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Linalool dehydratase/isomerase / Geraniol isomerase / Linalool dehydratase-isomerase / Myrcene hydratase


Mass: 41862.520 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Castellaniella defragrans (bacteria) / Gene: ldi / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E1XUJ2, linalool dehydratase, geraniol isomerase
#2: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#3: Chemical ChemComp-64Z / Geraniol / Geraniol


Mass: 154.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18O
#4: Chemical ChemComp-650 / Beta-Myrcene / Myrcene


Mass: 138.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 550 MME, bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97928 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 81656 / Num. obs: 957382 / % possible obs: 99.8 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rsym value: 0.014 / Net I/av σ(I): 13.7 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→49.08 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.223 4029 4.94 %
Rwork0.1785 --
obs0.1807 81564 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14590 0 93 121 14804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815122
X-RAY DIFFRACTIONf_angle_d0.92720541
X-RAY DIFFRACTIONf_dihedral_angle_d10.4398886
X-RAY DIFFRACTIONf_chiral_restr0.0542150
X-RAY DIFFRACTIONf_plane_restr0.0062662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.52930.42661440.37262570X-RAY DIFFRACTION97
2.5293-2.56020.31111360.27862646X-RAY DIFFRACTION100
2.5602-2.59260.34971460.26242655X-RAY DIFFRACTION100
2.5926-2.62670.30861360.25872625X-RAY DIFFRACTION100
2.6267-2.66270.34471490.29192626X-RAY DIFFRACTION100
2.6627-2.70070.40071260.3332648X-RAY DIFFRACTION99
2.7007-2.7410.30971420.26642635X-RAY DIFFRACTION100
2.741-2.78380.31241320.25372636X-RAY DIFFRACTION100
2.7838-2.82950.28251450.22542645X-RAY DIFFRACTION100
2.8295-2.87820.25121340.2132683X-RAY DIFFRACTION100
2.8782-2.93060.28161420.22212642X-RAY DIFFRACTION100
2.9306-2.98690.29481560.22072627X-RAY DIFFRACTION100
2.9869-3.04790.26051380.20642654X-RAY DIFFRACTION100
3.0479-3.11420.24791350.21742666X-RAY DIFFRACTION100
3.1142-3.18660.27751240.2142666X-RAY DIFFRACTION100
3.1866-3.26630.26441390.21072655X-RAY DIFFRACTION100
3.2663-3.35460.26481360.20852683X-RAY DIFFRACTION100
3.3546-3.45320.26591410.22812658X-RAY DIFFRACTION100
3.4532-3.56470.27691510.19382648X-RAY DIFFRACTION100
3.5647-3.6920.23921410.19642669X-RAY DIFFRACTION100
3.692-3.83980.1921540.16862670X-RAY DIFFRACTION100
3.8398-4.01450.19251350.15262660X-RAY DIFFRACTION99
4.0145-4.2260.1671250.13562691X-RAY DIFFRACTION100
4.226-4.49060.17451180.12992737X-RAY DIFFRACTION100
4.4906-4.83710.16961220.12592731X-RAY DIFFRACTION100
4.8371-5.32330.191370.14042717X-RAY DIFFRACTION100
5.3233-6.09240.18881400.15862740X-RAY DIFFRACTION100
6.0924-7.6710.17711470.15132783X-RAY DIFFRACTION100
7.671-49.08970.16181580.12942869X-RAY DIFFRACTION100
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)
17.8482-7.1544-0.95458.1883-0.35388.6270.18850.08260.66660.6129-0.3814-0.3482-0.7980.37540.25030.6685-0.12440.0360.3648-0.05050.437888.8031106.360685.053
24.59582.2973-1.08246.2071-1.25564.31260.05890.3862-0.3274-0.4544-0.19960.32870.2697-0.24460.15030.36180.0929-0.02550.3741-0.07130.38576.127690.532673.0323
32.1511-0.01870.324.6267-0.67613.65520.13840.1105-0.20410.25590.21040.81950.0096-0.5161-0.33120.35150.05120.10210.43210.03690.586165.434491.631883.4981
45.0451-0.71541.20862.7043-1.97255.68750.0934-0.3693-0.23970.62090.17590.8929-0.2742-0.404-0.22290.62820.10780.34530.49480.02150.816358.746895.72896.0253
52.2707-0.76063.39799.2722-0.51729.87250.1706-1.4969-0.35860.9205-0.07521.0152-0.6733-0.65340.0220.821-0.00030.21980.7038-0.00410.614770.970285.245109.209
62.07020.80250.41412.2445-1.13142.28090.1763-0.25730.0860.6601-0.10090.1387-0.3012-0.0085-0.07050.5734-0.00920.03250.3455-0.07520.344982.644295.408994.0699
74.06050.27750.57253.73191.214930.117-0.0275-0.05230.1580.0644-0.2393-0.0798-0.0144-0.18530.47820.02060.03640.3457-0.04320.352471.133364.253102.9492
85.46373.68361.14578.63350.83434.9635-0.04340.12980.31740.2028-0.09080.9175-0.0794-0.77630.14140.48090.04060.13990.4661-0.07590.46955.281158.1441106.9925
97.7733-5.227-4.05428.39265.20263.5821-0.35010.1243-0.80550.9669-0.17170.56710.5379-0.37210.54490.8061-0.02260.140.5406-0.02930.525662.475541.9075108.3148
102.227-0.3185-0.12234.1882-0.04992.8617-0.0303-0.2093-0.03430.62390.1812-0.39510.4350.4471-0.13550.68880.1136-0.10450.5694-0.09080.384980.306452.1466109.9597
117.29765.26512.88566.29632.86432.3505-0.36190.8415-0.7571-0.83580.4741-0.97360.21010.6053-0.15380.5938-0.00630.0920.4357-0.07720.555189.45834.718737.7025
122.1267-0.12780.70753.9054-0.67821.611-0.0942-0.16020.1407-0.08110.1350.65140.0739-0.3969-0.03350.3223-0.0794-0.04850.4887-0.00640.4966.604246.562945.7819
135.65093.73370.47166.7606-0.16990.5612-0.17420.18790.4472-0.96350.02290.72120.1516-0.2830.18410.5725-0.0314-0.20630.56530.05750.495168.345159.525928.5982
142.48840.5555-0.8713.5536-0.71282.4583-0.010.2248-0.007-0.49870.0337-0.03860.13080.0886-0.01990.3684-0.0011-0.00330.3618-0.05620.317684.824649.28835.7329
154.4023-3.87944.83125.9751-3.49415.53320.09170.74910.2452-0.56470.3436-0.1886-0.41970.5752-0.330.5062-0.12230.07780.6296-0.00880.391191.965787.877535.1953
160.9272-1.1737-1.88872.90241.6615.6560.0881-0.1523-0.21690.15480.04650.4540.47280.106-0.12210.3342-0.0269-0.08750.40550.02390.4977.274572.961746.1806
172.15450.0439-0.70592.46920.30748.0467-0.0894-0.03750.0398-0.0634-0.01380.5847-0.1746-0.66230.07060.3076-0.0017-0.10450.48230.05380.589368.255682.962748.9009
181.8539-1.519-2.46523.56722.00535.1919-0.0350.183-0.1625-0.3336-0.26330.9642-0.327-0.93270.33340.33780.0391-0.1760.6113-0.00930.733260.488289.858244.5863
196.89360.95735.46252.05511.72368.1133-0.0834-0.24570.4818-0.1987-0.02040.4873-0.5728-0.70.12290.42490.09-0.03130.38620.00210.573168.1948102.85553.9038
203.8464-1.0665-1.04814.4450.48164.2005-0.0463-0.08350.2753-0.12260.1883-0.2061-0.3260.1995-0.13810.3243-0.0752-0.0270.2841-0.00920.325886.995299.069850.3853
213.20111.3914-1.11525.44885.44577.9973-0.1279-0.2923-0.61510.30980.4614-0.46130.16921.0657-0.39610.31860.0879-0.04320.44730.04730.385590.743677.833948.7206
224.6924-0.369-3.31216.36471.88384.93140.17790.49380.1012-0.79030.18330.3682-0.189-0.2563-0.34640.371-0.0656-0.05320.36570.02840.401477.469489.900638.9265
234.78814.2524-4.61183.8262-4.05834.46330.0272-0.2677-0.61180.3898-0.2686-0.1330.20810.62450.23170.55370.0445-0.03170.48340.00990.501685.324719.793688.0972
242.7133-1.05872.20.8674-1.81723.891-0.0408-0.13370.28080.17870.0130.1746-0.25090.02830.0260.4673-0.0262-0.01030.4091-0.09560.53573.195140.176487.0182
252.23-0.72691.04694.28-2.11635.2012-0.06570.03370.2941-0.112-0.02840.3328-0.1728-0.65610.11440.3430.0130.01170.486-0.08380.614464.139534.997878.0853
264.7166-1.2833.40923.7939-2.35133.2346-0.1879-0.25570.10950.22960.23980.78890.1909-1.1776-0.05140.4092-0.02580.01810.6225-0.12730.701155.414227.872876.8526
276.89581.6804-4.56612.1265-0.8296.4769-0.14770.665-0.0009-0.36990.23510.42680.3624-0.5291-0.10650.3793-0.0427-0.11250.4548-0.01870.496763.710122.108962.1614
283.40431.20610.46012.222-0.37733.4621-0.02990.1171-0.1804-0.1643-0.0782-0.14150.26760.21280.11190.4610.04140.03110.3232-0.01050.441381.972420.71668.9009
291.9092-2.40940.43673.5779-0.64546.5195-0.1671-0.14630.30540.05130.2426-0.3122-0.32650.6321-0.03050.393-0.0222-0.04630.3313-0.0640.615686.486436.174483.3343
307.45310.9137-1.81757.3529-1.82772.42260.1483-0.9422-0.66310.6947-0.15630.57920.5837-0.1424-0.14370.4996-0.04310.01810.5451-0.01950.41271.186122.282383.1148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 210 )
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 366 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 122 )
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 162 )
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 237 )
10X-RAY DIFFRACTION10chain 'B' and (resid 238 through 366 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 24 )
12X-RAY DIFFRACTION12chain 'C' and (resid 25 through 162 )
13X-RAY DIFFRACTION13chain 'C' and (resid 163 through 237 )
14X-RAY DIFFRACTION14chain 'C' and (resid 238 through 365 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 24 )
16X-RAY DIFFRACTION16chain 'D' and (resid 25 through 59 )
17X-RAY DIFFRACTION17chain 'D' and (resid 60 through 122 )
18X-RAY DIFFRACTION18chain 'D' and (resid 123 through 162 )
19X-RAY DIFFRACTION19chain 'D' and (resid 163 through 237 )
20X-RAY DIFFRACTION20chain 'D' and (resid 238 through 319 )
21X-RAY DIFFRACTION21chain 'D' and (resid 320 through 341 )
22X-RAY DIFFRACTION22chain 'D' and (resid 342 through 365 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 24 )
24X-RAY DIFFRACTION24chain 'E' and (resid 25 through 59 )
25X-RAY DIFFRACTION25chain 'E' and (resid 60 through 122 )
26X-RAY DIFFRACTION26chain 'E' and (resid 123 through 162 )
27X-RAY DIFFRACTION27chain 'E' and (resid 163 through 237 )
28X-RAY DIFFRACTION28chain 'E' and (resid 238 through 319 )
29X-RAY DIFFRACTION29chain 'E' and (resid 320 through 341 )
30X-RAY DIFFRACTION30chain 'E' and (resid 342 through 366 )

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