[English] 日本語
Yorodumi
- PDB-1nww: Limonene-1,2-epoxide hydrolase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nww
TitleLimonene-1,2-epoxide hydrolase
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolase
Function / homology
Function and homology information


limonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity
Similarity search - Function
Limonene-1,2-epoxide hydrolase / Limonene-1,2-epoxide hydrolase catalytic domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
HEPTANAMIDE / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsArand, M. / Hallberg, B.M. / Zou, J. / Bergfors, T. / Oesch, F. / van der Werf, M.J. / de Bont, J.A.M. / Jones, T.A. / Mowbray, S.L.
CitationJournal: EMBO J. / Year: 2003
Title: Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site
Authors: Arand, M. / Hallberg, B.M. / Zou, J. / Bergfors, T. / Oesch, F. / van der Werf, M.J. / de Bont, J.A.M. / Jones, T.A. / Mowbray, S.L.
History
DepositionFeb 7, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5235
Polymers33,0692
Non-polymers4543
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-2 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.548, 47.652, 129.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Limonene-1,2-epoxide hydrolase


Mass: 16534.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: DCL14 / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase
#2: Chemical ChemComp-HPN / HEPTANAMIDE


Mass: 129.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 6000, LiCl, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112.8 mg/mlprotein1drop
210 mMHEPES1droppH7.0
330 %PEG60001reservoir
41 M1reservoirLiCl
50.1 MMES1reservoirpH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 1999
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.2→64.6 Å / Num. all: 89183 / Num. obs: 88916 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.063 / Net I/σ(I): 28.2
Reflection shellResolution: 1.2→1.21 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.272 / % possible all: 94.1
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.272

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBV. 2.1phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD
Starting model: Model from structure solution using SAD on Se-Met labelled protein. SAD data collected at ESRF beamline ID14-1 at 0.934 A wavelength.

Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.201 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17451 4306 4.8 %RANDOM
Rwork0.14686 ---
all0.14822 84491 --
obs0.14822 84491 100 %-
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: 13.873 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 30 378 2713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222387
X-RAY DIFFRACTIONr_bond_other_d0.0020.022182
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.983257
X-RAY DIFFRACTIONr_angle_other_deg3.18135093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.023301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78415416
X-RAY DIFFRACTIONr_chiral_restr0.1270.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02479
X-RAY DIFFRACTIONr_nbd_refined0.2170.3446
X-RAY DIFFRACTIONr_nbd_other0.1990.32147
X-RAY DIFFRACTIONr_nbtor_other0.2740.512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.5244
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0640.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5690.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.522
X-RAY DIFFRACTIONr_mcbond_it1.8991.51467
X-RAY DIFFRACTIONr_mcangle_it2.77822376
X-RAY DIFFRACTIONr_scbond_it3.7393920
X-RAY DIFFRACTIONr_scangle_it5.314.5875
X-RAY DIFFRACTIONr_rigid_bond_restr1.82522387
X-RAY DIFFRACTIONr_sphericity_free15.4395380
X-RAY DIFFRACTIONr_sphericity_bonded6.67952335
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.178 291
Rwork0.162 5899
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.172 / Rfactor Rwork: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.025
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more