[English] 日本語
Yorodumi
- PDB-5mxp: Haloalkane dehalogenase DmxA from Marinobacter sp. ELB17 possessi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mxp
TitleHaloalkane dehalogenase DmxA from Marinobacter sp. ELB17 possessing a unique catalytic residue
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / thermostable enzyme / disulfide bridge / unique catalytic residue
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
ACETATE ION / Alpha/beta hydrolase
Similarity search - Component
Biological speciesMarinobacter sp. ELB17 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTratsiak, K. / Rezacova, P. / Prudnikova, T.
Funding support Czech Republic, 9items
OrganizationGrant numberCountry
Grant AgencyP207/12/0775 Czech Republic
Grant AgencyGA16-24223S Czech Republic
Grant AgencyGA16-06096S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLO1214 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLO1304 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLQ1605 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015051 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015047 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015055 Czech Republic
CitationJournal: Microorganisms / Year: 2019
Title: Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic BacteriumMarinobactersp. ELB17.
Authors: Chrast, L. / Tratsiak, K. / Planas-Iglesias, J. / Daniel, L. / Prudnikova, T. / Brezovsky, J. / Bednar, D. / Kuta Smatanova, I. / Chaloupkova, R. / Damborsky, J.
History
DepositionJan 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,20713
Polymers69,8452
Non-polymers36111
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-96 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.371, 78.343, 150.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Alpha/beta hydrolase / DmxA


Mass: 34922.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: psychrophilic / Source: (gene. exp.) Marinobacter sp. ELB17 (bacteria) / Gene: MELB17_23105 / Plasmid: pET21b / Details (production host): Novagen, USA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DH5a / References: UniProt: A3JB27, haloalkane dehalogenase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 1.89 Å3/Da / Density % sol: 34.85 % / Description: rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M ammonium acetate, 30%(w/v) PEG 4000 and 0.1M sodium citrate tribasic dihydrate, additionally added sarcosine

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid-nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 24, 2013 / Details: silicon pixel array detector
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 86980 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.28 % / Biso Wilson estimate: 21.048 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 8.02
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 5.52 % / Rmerge(I) obs: 0.621 / Num. unique obs: 5978 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDS2013-03-30data reduction
XDS2013-03-30data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+46 / Resolution: 1.45→75.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.379 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0742 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.079
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 4589 5 %RANDOM
Rwork0.1732 ---
obs0.1752 86980 99.71 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.68 Å2 / Biso mean: 18.624 Å2 / Biso min: 7.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.45→75.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 21 603 5394
Biso mean--26.43 27.99 -
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195017
X-RAY DIFFRACTIONr_bond_other_d0.0020.024500
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.956827
X-RAY DIFFRACTIONr_angle_other_deg1.098310461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76923.566258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15115810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9181538
X-RAY DIFFRACTIONr_chiral_restr0.1250.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215649
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021081
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 329 -
Rwork0.28 6373 -
all-6702 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.81330.01-0.20430.8861-0.10971.056-0.001-0.01150.0270.05040.0276-0.0631-0.10910.0071-0.02670.14470.00060.00260.0013-0.00110.0193-40.35618.37355.966
21.30040.2021-0.56260.9037-0.23971.4580.022-0.02060.05810.0276-0.00810.0310.01760.0211-0.01380.130.00760.00410.0009-0.00080.0293-19.31817.51419.625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 296
2X-RAY DIFFRACTION2B3 - 296

+
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://pdbjlvh1.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