[English] 日本語
Yorodumi
- PDB-2cjp: Structure of potato (Solanum tuberosum) epoxide hydrolase I (StEH1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cjp
TitleStructure of potato (Solanum tuberosum) epoxide hydrolase I (StEH1)
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-PROPYLPENTANAMIDE / Epoxide hydrolase
Similarity search - Component
Biological speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMowbray, S.L. / Elfstrom, L.T. / Ahlgren, K.M. / Andersson, C.E. / Widersten, M.
CitationJournal: Protein Sci. / Year: 2006
Title: X-Ray Structure of Potato Epoxide Hydrolase Sheds Light on Substrate Specificity in Plant Enzymes.
Authors: Mowbray, S.L. / Elfstrom, L.T. / Ahlgren, K.M. / Andersson, C.E. / Widersten, M.
History
DepositionApr 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPOXIDE HYDROLASE
B: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7115
Polymers74,3112
Non-polymers4003
Water7,296405
1
A: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3502
Polymers37,1561
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3613
Polymers37,1561
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.926, 98.532, 122.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.7035, 0.6653, -0.2501), (0.691, -0.5578, 0.4598), (0.1664, -0.4963, -0.8521)
Vector: -19.8967, 106.9727, 85.4732)

-
Components

#1: Protein EPOXIDE HYDROLASE


Mass: 37155.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Strain: LEMHI RUSSET / Plasmid: PGTACSTEH1-5H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q41415, epoxide hydrolase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-VPR / 2-PROPYLPENTANAMIDE / VALPROMIDE


Mass: 143.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% ...Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% PEG 10, 000), AND EQUILIBRATED BY SITTING-DROP VAPOR DIFFUSION AT ROOM TEMPERATURE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→31.6 Å / Num. obs: 49514 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.1 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VJ5

1vj5


Resolution: 1.95→31.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.577 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 OF THE A CHAIN, AND 2-3 OF THE B CHAIN WERE OMITTED BECAUSE OF DISORDER. THE PROTEIN WAS EXPRESSED WITH AN ADDITIONAL SEQUENCE AT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 OF THE A CHAIN, AND 2-3 OF THE B CHAIN WERE OMITTED BECAUSE OF DISORDER. THE PROTEIN WAS EXPRESSED WITH AN ADDITIONAL SEQUENCE AT THE C-TERMINUS, TSHHHHH, WHICH WAS ALSO NOT VISIBLE IN THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2510 5.1 %RANDOM
Rwork0.203 ---
obs0.205 47002 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--2.73 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5115 0 27 405 5547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9537202
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2485637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02523.833240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82215844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7441520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.22384
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23529
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2378
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4751.53276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82325142
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.95732340
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5124.52060
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 178
Rwork0.286 3369

+
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