[English] 日本語
Yorodumi
- PDB-4bb0: Structure of a putative epoxide hydrolase Q244E mutant from Pseud... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bb0
TitleStructure of a putative epoxide hydrolase Q244E mutant from Pseudomonas aeruginosa, with bound MFA.
ComponentsPROBABLE EPOXIDE 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
fluoroacetic acid / Probable epoxide hydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSchmidberger, J.W. / Schnell, R. / Schneider, G.
CitationJournal: To be Published
Title: Structure of a Putative Epoxide Hydrolase Mutant
Authors: Schmidberger, J.W. / Schnell, R. / Schneider, G.
History
DepositionSep 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,16018
Polymers33,6171
Non-polymers1,54317
Water4,504250
1
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules

A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,32036
Polymers67,2342
Non-polymers3,08634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7800 Å2
ΔGint-268.2 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.242, 83.242, 140.541
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2137-

HOH

-
Components

#1: Protein PROBABLE EPOXIDE HYDROLASE


Mass: 33616.965 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9I229
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3FO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMONOFLUOROACETIC ACID (MFA): STRUCTURE IS RESULT OF A 100 MM SOAK IN MFA FOR 30 MIN.
Sequence detailsCLONING AND CUTTING OF THE HIS TAG LEAVES AND EXTRA N- TERMINAL SERINE. THIS MODEL IS A Q244E MUTANT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.5 %
Description: THIS MODEL WAS ACTUALLY SOLVED BY REFINING THE DATA AGAINST THE NATIVE MODEL OF PA2086 USING REFMAC.
Crystal growpH: 8.5
Details: 0.1 M LI2 SO4, 1.25 M (NH4)2SO4, 0.1 M TRIS HCL PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.04088
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 1.77→29.15 Å / Num. obs: 48281 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B9A

4b9a


Resolution: 1.77→27.16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.43 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21522 2442 5.1 %RANDOM
Rwork0.15092 ---
obs0.15418 45752 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.77→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 85 250 2663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192500
X-RAY DIFFRACTIONr_bond_other_d0.0010.022307
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9773411
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0015252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74921.935124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74515367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121529
X-RAY DIFFRACTIONr_chiral_restr0.1170.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
X-RAY DIFFRACTIONr_nbd_refined0.2520.2764
X-RAY DIFFRACTIONr_nbd_other0.2210.21892
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21113
X-RAY DIFFRACTIONr_nbtor_other0.1080.21108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.180.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.30934805
X-RAY DIFFRACTIONr_sphericity_free34.654588
X-RAY DIFFRACTIONr_sphericity_bonded15.46354917
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 187 -
Rwork0.253 3348 -
obs--99.55 %

+
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