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- PDB-8b5o: Structure of haloalkane dehalogenase DmmarA from Mycobacterium ma... -

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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 / homologyEpoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / ACETATE ION / FORMIC ACID / Haloalkane dehalogenase DhaA
Function and homology information
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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