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- PDB-8b6o: X-ray structure of the haloalkane dehalogenase HaloTag7 circular ... -

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Basic information

Entry
Database: PDB / ID: 8b6o
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 circular permutated at positions 141-156 (cpHaloTagDelta) fused to M13
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein / M13
Function / homologyHaloalkane dehalogenase, subfamily 2 / haloalkane dehalogenase / haloalkane dehalogenase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / response to toxic substance / Alpha/Beta hydrolase fold / Haloalkane dehalogenase
Function and homology information
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTarnawski, M. / Johnsson, K. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: X-ray structure of the haloalkane dehalogenase HaloTag7 circular permutated at positions 141-156 (cpHaloTagDelta) fused to M13
Authors: Tarnawski, M. / Johnsson, K. / Hiblot, J.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7562
Polymers35,7211
Non-polymers351
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.600, 81.320, 153.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 35720.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium acetate pH 4.5, 0.65 M sodium dihydrogen phosphate, 1.00 M dipotassium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99995 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19257 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 41.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 25.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.81 / Num. unique obs: 2577 / CC1/2: 0.897 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292125777

Resolution: 2→40.66 Å / SU ML: 0.2622 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.4036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 963 5 %
Rwork0.2214 18292 -
obs0.2228 19255 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.5 Å2
Refinement stepCycle: LAST / Resolution: 2→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 1 47 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272388
X-RAY DIFFRACTIONf_angle_d0.61553260
X-RAY DIFFRACTIONf_chiral_restr0.0433349
X-RAY DIFFRACTIONf_plane_restr0.0045425
X-RAY DIFFRACTIONf_dihedral_angle_d4.2673312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.34631360.30672592X-RAY DIFFRACTION100
2.11-2.240.34041350.28662560X-RAY DIFFRACTION99.96
2.24-2.410.33961350.28852568X-RAY DIFFRACTION100
2.41-2.650.28151360.26472584X-RAY DIFFRACTION100
2.65-3.040.31291370.25232611X-RAY DIFFRACTION99.85
3.04-3.820.25431390.21582637X-RAY DIFFRACTION99.82
3.83-40.660.19181450.1812740X-RAY DIFFRACTION99.62
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)
15.18678557721-2.891115113072.626149187386.763516534192.853796348485.74950803868-0.1197336782690.393745348980.8252193786830.179396880349-0.1224466328260.957329839135-0.527111629737-0.401143130740.1864952872420.412245887986-0.06439074836710.009002903777350.5299387798460.04945754387480.577070132573-25.1402789351-8.69954194918-32.9641250558
22.50013965745-0.3113995849612.048766081221.877119604230.9287117610616.80119566643-0.1596862149210.243011155560.02781046743520.0546746077936-0.1523705231220.05593783075360.03545141614930.3049454453260.2286771460410.275176260484-0.05581507967120.02865964203930.2409799686220.1385006861110.322243511616-14.1677243068-10.020808854-24.2628391153
30.990276265348-1.22359403769-0.7168014129851.82491979859-0.1048837834633.69933695536-0.08122146839840.1360072816940.4390066441690.002774937978150.29475204953-0.0769797758223-0.8480257173670.541362854240.1005406197130.805206102568-0.394890321939-0.1545620384750.6450184848840.3067166565840.723639007597-3.008158948246.10960837612-20.5584059018
42.94884063824-0.3797492147952.254797048292.370137498120.2605095995995.90431478370.03000467851590.561860407842-0.1992218647270.366255186930.126042445176-0.3650489023050.7694609377441.26069561036-0.04356540542910.4165670048260.0945918810668-0.002333441922620.5111720813950.06734551564440.387438612987-3.33433163724-16.5996629295-17.6732630838
54.596905178880.4746764242572.424613060642.250230864142.446648894636.61414645718-0.163359008612-0.1060022795790.1022862917790.316718582947-0.05737790732620.08704017770170.04190858599220.3167382619990.161696070050.31265371014-0.05192400344260.03420640229970.2755548871930.1124627633060.324529640335-11.0659508125-7.86499170856-12.0293797195
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 38 )9 - 381 - 30
22chain 'A' and (resid 39 through 123 )39 - 12331 - 115
33chain 'A' and (resid 124 through 141 )124 - 141116 - 133
44chain 'A' and (resid 142 through 262 )142 - 262134 - 232
55chain 'A' and (resid 263 through 321 )263 - 321233 - 291

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