[English] 日本語
Yorodumi
- PDB-5flk: Structure of haloalkane dehalogenase variant DhaA101 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5flk
TitleStructure of haloalkane dehalogenase variant DhaA101
ComponentsDHAA101
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE / ALPHA/BETA-HYDROLASE
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / 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
DI(HYDROXYETHYL)ETHER / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRHODOCOCCUS RHODOCHROUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsChaloupkova, R. / Waterman, J. / Damborsky, J.
CitationJournal: To be Published
Title: Evolutionary Analysis is a Powerful Complement to Energy Calculations Allowing Entropy-Driven Stabilization
Authors: Beerens, K. / Mazurenko, S. / Kunka, A. / Marques, S.M. / Hansen, N. / Musil, M. / Chaloupkova, R. / Waterman, J. / Brezovsky, J. / Bednar, D. / Prokop, Z. / Damborsky, J.
History
DepositionOct 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: DHAA101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6414
Polymers34,2341
Non-polymers4073
Water5,693316
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.660, 44.400, 46.260
Angle α, β, γ (deg.)115.26, 97.59, 109.52
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein DHAA101


Mass: 34234.008 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS RHODOCHROUS (bacteria) / Strain: NCIMB13064 / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.08 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M MES/IMIDAZOLE PH 6.5, 10% (W/V) PEG 20000, 20% (V/V) PEG MME 500, 0.2 M DL-GLUTAMATIC ACID MONOHYDRATE, 0.02M DL-ALANINE, 0.02M GLYCINE, 0.02M DL-LYSINE ...Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M MES/IMIDAZOLE PH 6.5, 10% (W/V) PEG 20000, 20% (V/V) PEG MME 500, 0.2 M DL-GLUTAMATIC ACID MONOHYDRATE, 0.02M DL-ALANINE, 0.02M GLYCINE, 0.02M DL-LYSINE MONOHYDROCHLORIDE AND 0.02M DL-SERINE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 0.99→39.61 Å / Num. obs: 107099 / % possible obs: 70.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.2
Reflection shellResolution: 0.99→1.02 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 6.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E46

4e46


Resolution: 0.99→39.61 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.575 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.12973 5283 4.9 %RANDOM
Rwork0.11405 ---
obs0.11483 101816 70.18 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.32 Å20.41 Å2
2---0.15 Å20.21 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 0.99→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 26 316 2699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192689
X-RAY DIFFRACTIONr_bond_other_d0.0030.022546
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.973715
X-RAY DIFFRACTIONr_angle_other_deg1.21235922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55523.333135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01115427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.151522
X-RAY DIFFRACTIONr_chiral_restr0.1260.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213040
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02626
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2811.091236
X-RAY DIFFRACTIONr_mcbond_other1.0691.0861235
X-RAY DIFFRACTIONr_mcangle_it1.6741.6491560
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8861.3681453
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3481.9642126
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.75635235
X-RAY DIFFRACTIONr_sphericity_free28.241559
X-RAY DIFFRACTIONr_sphericity_bonded9.25755377
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 32 -
Rwork0.317 704 -
obs--6.51 %

+
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