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- PDB-8b6n: X-ray structure of the haloalkane dehalogenase HaloTag7 circular ... -

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Basic information

Entry
Database: PDB / ID: 8b6n
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 circular permutated at positions 141-156 (cpHaloTagDelta)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTarnawski, M. / Johnsson, K. / Hiblot, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Science / Year: 2024
Title: Recording physiological history of cells with chemical labeling.
Authors: Huppertz, M.C. / Wilhelm, J. / Grenier, V. / Schneider, M.W. / Falt, T. / Porzberg, N. / Hausmann, D. / Hoffmann, D.C. / Hai, L. / Tarnawski, M. / Pino, G. / Slanchev, K. / Kolb, I. / Acuna, ...Authors: Huppertz, M.C. / Wilhelm, J. / Grenier, V. / Schneider, M.W. / Falt, T. / Porzberg, N. / Hausmann, D. / Hoffmann, D.C. / Hai, L. / Tarnawski, M. / Pino, G. / Slanchev, K. / Kolb, I. / Acuna, C. / Fenk, L.M. / Baier, H. / Hiblot, J. / Johnsson, K.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)32,7822
Polymers32,5751
Non-polymers2071
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint5 kcal/mol
Surface area11060 Å2
Unit cell
Length a, b, c (Å)45.850, 79.320, 154.180
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: 32575.094 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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M CHES pH 9.5, 1.0 M trisodium citrate with 40% (v/v) polypropylene glycol P400 additive

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97797 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12786 / % possible obs: 99.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 52.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.83
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1438 / CC1/2: 0.768 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y2X

5y2x


Resolution: 2.3→39.7 Å / SU ML: 0.4627 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.2934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 640 5.01 %
Rwork0.2146 12141 -
obs0.2165 12781 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 13 13 2189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392246
X-RAY DIFFRACTIONf_angle_d0.65883069
X-RAY DIFFRACTIONf_chiral_restr0.0478330
X-RAY DIFFRACTIONf_plane_restr0.0058400
X-RAY DIFFRACTIONf_dihedral_angle_d9.6008297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.46331220.40782310X-RAY DIFFRACTION96.47
2.48-2.730.33821270.29592408X-RAY DIFFRACTION99.76
2.73-3.120.30311270.27282418X-RAY DIFFRACTION99.69
3.12-3.930.22711290.21372454X-RAY DIFFRACTION99.81
3.93-39.70.21011350.16212551X-RAY DIFFRACTION99.7
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)
12.518358760361.189842662231.610358153852.321354982241.130581943375.086509901060.01311867021170.140550276017-0.008036555849610.07038619154770.005437495112150.1516053431450.168079711196-0.06118102076690.01339110931970.327964146230.03409194729820.02301544402060.299576526960.04785428161890.387951439657-17.1998031309-10.3726568505-25.7062089781
21.031490064360.7372134191771.451997485590.5406715358291.071410711682.07467927416-0.4118105870940.7070662346770.278754733263-0.161716557610.379187656730.0422426118187-1.156399333211.348644494840.1176284674960.571425629671-0.2704011412250.001980690381860.7116979031450.0509773969780.463196829629-3.87046861615.07906853815-21.7036913713
31.961908028610.9025207138091.662850368171.781583504520.7663314990374.077509784960.02512593921590.434172498697-0.2562377712740.1756014265480.350600641429-0.3981463936350.482060801591.2004044223-0.33687721730.4465195043020.148813908946-0.03363225329140.671056804054-0.1012600346580.475149228631-2.34714784794-13.9764244417-19.2087620117
43.119169598821.37981377603-0.6049193859882.742428688641.741586537185.728627557270.0669711537433-0.1245253872990.02361071926220.4435922105420.158684907271-0.1256382827840.1878375588220.529906732108-0.2163889551010.4065502855260.03826138310770.01207797593980.334989336774-0.03949440981780.409800352122-9.32390988641-7.38088301972-11.5307322777
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 2 through 77 )2 - 771 - 76
22chain 'A' and (resid 78 through 104 )78 - 10477 - 103
33chain 'A' and (resid 105 through 233 )105 - 233104 - 215
44chain 'A' and (resid 234 through 290 )234 - 290216 - 272

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