[English] 日本語
Yorodumi
- PDB-4r9k: Structure of thermostable eightfold mutant of limonene epoxide hy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r9k
TitleStructure of thermostable eightfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / limonene epoxide hydrolase / NTF-2 fold / engineered / thermostable
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
(2R)-2-hydroxyhexanamide / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFloor, R.J. / Wijma, H.J. / Jekel, P.A. / Terwisscha van Scheltinga, A.C. / Dijkstra, B.W. / Janssen, D.B.
CitationJournal: Proteins / Year: 2015
Title: X-ray crystallographic validation of structure predictions used in computational design for protein stabilization.
Authors: Floor, R.J. / Wijma, H.J. / Jekel, P.A. / Terwisscha van Scheltinga, A.C. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,30011
Polymers58,4463
Non-polymers8548
Water6,521362
1
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5037
Polymers38,9642
Non-polymers5395
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-6 kcal/mol
Surface area13190 Å2
MethodPISA
2
C: Limonene-1,2-epoxide hydrolase
hetero molecules

C: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5958
Polymers38,9642
Non-polymers6316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3800 Å2
ΔGint-6 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.049, 88.049, 110.241
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-338-

HOH

-
Components

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


Mass: 19482.072 Da / Num. of mol.: 3 / Mutation: S15P, A19K, E45K, T76K, T85V, N92K, Y96F, E124D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HYH / (2R)-2-hydroxyhexanamide


Mass: 131.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 1.44 M tri-sodium citrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.45→76.253 Å / Num. obs: 87794 / % possible obs: 99.9 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 9.9 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.024 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.45-1.53100.9022.9126480.29699.6
4.59-44.679.50.02755.429910.00999.9

-
Processing

Software
NameVersionClassification
tvxdata collection
PHASERphasing
REFMAC5.8.0071refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NWW

1nww


Resolution: 1.5→44 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.002 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16476 4008 5 %RANDOM
Rwork0.14143 ---
obs0.14261 75382 99.89 %-
all-75382 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.991 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å2-0 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 57 362 4025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023754
X-RAY DIFFRACTIONr_bond_other_d0.0010.023627
X-RAY DIFFRACTIONr_angle_refined_deg2.2751.9925077
X-RAY DIFFRACTIONr_angle_other_deg0.97638385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8324.545165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72715646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5871521
X-RAY DIFFRACTIONr_chiral_restr0.160.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02807
X-RAY DIFFRACTIONr_mcbond_it1.7481.6121843
X-RAY DIFFRACTIONr_mcbond_other1.7291.611842
X-RAY DIFFRACTIONr_mcangle_it2.4682.4092301
X-RAY DIFFRACTIONr_mcangle_other2.4812.4112302
X-RAY DIFFRACTIONr_scbond_it3.3441.9471911
X-RAY DIFFRACTIONr_scbond_other3.3431.9481912
X-RAY DIFFRACTIONr_scangle_other4.9422.7822772
X-RAY DIFFRACTIONr_long_range_B_refined5.97914.1364447
X-RAY DIFFRACTIONr_long_range_B_other5.97914.144448
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 302 -
Rwork0.201 5491 -
obs--99.62 %

+
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