[English] 日本語
Yorodumi
- PDB-8b5o: Structure of haloalkane dehalogenase DmmarA from Mycobacterium ma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b5o
TitleStructure of haloalkane dehalogenase DmmarA from Mycobacterium marinum at pH 5.5
ComponentsHaloalkane dehalogenase DhaA
KeywordsHYDROLASE / haloalkane dehalogenase / enzyme
Function / homology
Function and homology information


catalytic activity / membrane
Similarity search - Function
: / 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 / FORMIC ACID / Haloalkane dehalogenase DhaA
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.597 Å
AuthorsSnajdarova, K. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation22-09853S Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum.
Authors: Snajdarova, K. / Marques, S.M. / Damborsky, J. / Bednar, D. / Marek, M.
History
DepositionSep 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haloalkane dehalogenase DhaA
B: Haloalkane dehalogenase DhaA
C: Haloalkane dehalogenase DhaA
D: Haloalkane dehalogenase DhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,20825
Polymers132,9064
Non-polymers1,30221
Water12,755708
1
A: Haloalkane dehalogenase DhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5957
Polymers33,2261
Non-polymers3686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase DhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6087
Polymers33,2261
Non-polymers3816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Haloalkane dehalogenase DhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7339
Polymers33,2261
Non-polymers5068
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Haloalkane dehalogenase DhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2722
Polymers33,2261
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.699, 60.766, 104.777
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Haloalkane dehalogenase DhaA


Mass: 33226.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Gene: dhaA, MMAR_4113 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HR89
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: ammonium acetate, Bis-Tris, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.597→47.71 Å / Num. obs: 144169 / % possible obs: 98.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1 / Resolution: 1.6→1.62 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.91.29168920.490.5651.41496
6.40.0429490.9980.0180.04698.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B5K

8b5k


Resolution: 1.597→43.702 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 7081 4.91 %
Rwork0.1977 137035 -
obs0.1997 144116 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.14 Å2 / Biso mean: 29.3224 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 1.597→43.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8883 0 85 710 9678
Biso mean--42.39 32.29 -
Num. residues----1126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5974-1.61550.34682080.3126437595
1.6155-1.63450.292200.2857450398
1.6345-1.65440.29252490.2623451998
1.6544-1.67540.29832470.2606443798
1.6754-1.69740.31492520.2597448398
1.6974-1.72070.2942370.2488452399
1.7207-1.74530.26292260.2309456198
1.7453-1.77130.27112300.2245452799
1.7713-1.7990.27312340.2274450998
1.799-1.82850.27032130.222462099
1.8285-1.860.2882310.2297454299
1.86-1.89390.27712130.2293455899
1.8939-1.93030.30712180.2542453699
1.9303-1.96970.25162170.2067455398
1.9697-2.01250.23232350.20714602100
2.0125-2.05930.27662680.2084453699
2.0593-2.11080.27062160.2104451898
2.1108-2.16790.24012680.1896458699
2.1679-2.23170.22332370.19384590100
2.2317-2.30370.26252490.2079451699
2.3037-2.3860.2292260.1902464499
2.386-2.48160.22622710.18924553100
2.4816-2.59450.22412540.18654593100
2.5945-2.73130.22812480.19044608100
2.7313-2.90240.23882160.18584648100
2.9024-3.12640.24012430.18924606100
3.1264-3.44090.20072330.17784644100
3.4409-3.93850.23652410.18074652100
3.9385-4.9610.19522310.16764708100
4.961-43.7020.20892500.18784785100
Refinement TLS params.Method: refined / Origin x: 36.9065 Å / Origin y: -7.0357 Å / Origin z: 26.7306 Å
111213212223313233
T0.1874 Å2-0.0154 Å2-0.0172 Å2-0.0931 Å20.0058 Å2--0.0981 Å2
L0.2123 °2-0.0212 °2-0.0351 °2-0.3652 °2-0.0222 °2--0.3599 °2
S0.0204 Å °0.0251 Å °-0.0198 Å °-0.1464 Å °0.0167 Å °0.0519 Å °0.0523 Å °-0.0168 Å °-0.024 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 501
2X-RAY DIFFRACTION1allA601 - 901
3X-RAY DIFFRACTION1allB1 - 801
4X-RAY DIFFRACTION1allB901 - 1001
5X-RAY DIFFRACTION1allC1 - 301
6X-RAY DIFFRACTION1allC401 - 501
7X-RAY DIFFRACTION1allC601
8X-RAY DIFFRACTION1allC701 - 901
9X-RAY DIFFRACTION1allC1001
10X-RAY DIFFRACTION1allC1101
11X-RAY DIFFRACTION1allD1 - 301
12X-RAY DIFFRACTION1allF1 - 714

+
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