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- PDB-8b5k: Structure of haloalkane dehalogenase DmmarA from Mycobacterium ma... -

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Basic information

Entry
Database: PDB / ID: 8b5k
TitleStructure of haloalkane dehalogenase DmmarA from Mycobacterium marinum at pH 6.5
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 / FORMIC ACID / Haloalkane dehalogenase DhaA
Function and homology information
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.849 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

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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)134,46122
Polymers132,9064
Non-polymers1,55518
Water10,431579
1
A: Haloalkane dehalogenase DhaA
B: Haloalkane dehalogenase DhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0059
Polymers66,4532
Non-polymers5537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Haloalkane dehalogenase DhaA
D: Haloalkane dehalogenase DhaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,45613
Polymers66,4532
Non-polymers1,00311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.816, 61.381, 106.689
Angle α, β, γ (deg.)90.000, 106.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 597 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: potassium phosphate, Bis-Tris propane, 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: 1.849→48.37 Å / Num. obs: 97565 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1 / Resolution: 1.85→1.88 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.81.66246390.3830.741.82597.1
6.30.0346380.9990.0140.03798.9

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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: 1MJ5

1mj5


Resolution: 1.849→44.073 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 4800 4.92 %
Rwork0.191 92678 -
obs0.1935 97478 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.71 Å2 / Biso mean: 28.1315 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 1.849→44.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8959 0 102 579 9640
Biso mean--43.26 32.87 -
Num. residues----1135
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8494-1.87050.37891520.3443298695
1.8705-1.89250.32451730.31062986100
1.8925-1.91560.36161720.30163109100
1.9156-1.93980.38631590.29713025100
1.9398-1.96530.27681730.26333062100
1.9653-1.99220.29551530.24453062100
1.9922-2.02070.31671590.25043086100
2.0207-2.05090.3281650.24923123100
2.0509-2.08290.3061280.24873059100
2.0829-2.11710.31241510.22983116100
2.1171-2.15360.30191540.2233049100
2.1536-2.19270.28651550.21813113100
2.1927-2.23490.27941590.223056100
2.2349-2.28050.29921520.22593116100
2.2805-2.33010.26261520.20783040100
2.3301-2.38430.30111490.20113122100
2.3843-2.44390.26161450.20543099100
2.4439-2.510.27441740.2013080100
2.51-2.58380.25581580.20343094100
2.5838-2.66720.26171610.19623101100
2.6672-2.76260.2591530.20113098100
2.7626-2.87310.26121650.18923084100
2.8731-3.00390.23871760.19353089100
3.0039-3.16220.25021720.19763092100
3.1622-3.36030.23411590.17583100100
3.3603-3.61960.20451570.16433140100
3.6196-3.98360.18191580.14913110100
3.9836-4.55960.15521610.1313110100
4.5596-5.74260.18371820.14063139100
5.7426-44.0730.1911730.16093232100
Refinement TLS params.Method: refined / Origin x: 36.2516 Å / Origin y: -6.9044 Å / Origin z: 26.7575 Å
111213212223313233
T0.2614 Å2-0.0021 Å20.0074 Å2-0.1224 Å2-0.002 Å2--0.1343 Å2
L0.2385 °20.0009 °20.0577 °2-0.2788 °2-0.0128 °2--0.2028 °2
S0.009 Å °-0.0097 Å °-0.0075 Å °-0.124 Å °-0.0001 Å °0.0187 Å °0.053 Å °0.0191 Å °-0.0095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 284
2X-RAY DIFFRACTION1allA301 - 501
3X-RAY DIFFRACTION1allA601
4X-RAY DIFFRACTION1allB1 - 284
5X-RAY DIFFRACTION1allB301 - 601
6X-RAY DIFFRACTION1allB801
7X-RAY DIFFRACTION1allC1 - 284
8X-RAY DIFFRACTION1allC401 - 1301
9X-RAY DIFFRACTION1allC1401 - 1501
10X-RAY DIFFRACTION1allC1601
11X-RAY DIFFRACTION1allD1 - 501
12X-RAY DIFFRACTION1allF1 - 584

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