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- PDB-8b6p: X-ray structure of the haloalkane dehalogenase HaloTag7 circular ... -

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Basic information

Entry
Database: PDB / ID: 8b6p
TitleX-ray structure of the haloalkane dehalogenase HaloTag7 circular permutated at positions 154-156 (cpHaloTag7_154-156)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / HaloTag / HaloTag7 / Self-Labeling Protein
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: 1.1 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

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6174
Polymers68,5462
Non-polymers712
Water12,250680
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3082
Polymers34,2731
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3082
Polymers34,2731
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.870, 94.660, 100.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34272.938 Da / Num. of mol.: 2
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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Bicine pH 9.0, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 251839 / % possible obs: 95.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 8.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.68
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 8.49 / Num. unique obs: 54597 / CC1/2: 0.965 / % possible all: 90.8

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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: 1.1→42.79 Å / SU ML: 0.0651 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 11.6472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.149 12591 5 %
Rwork0.137 239241 -
obs0.1376 251832 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.99 Å2
Refinement stepCycle: LAST / Resolution: 1.1→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 2 680 5392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00984897
X-RAY DIFFRACTIONf_angle_d1.16546696
X-RAY DIFFRACTIONf_chiral_restr0.098707
X-RAY DIFFRACTIONf_plane_restr0.0134883
X-RAY DIFFRACTIONf_dihedral_angle_d5.6112644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.14213360.12516396X-RAY DIFFRACTION77.13
1.11-1.130.1373830.1157277X-RAY DIFFRACTION87.66
1.13-1.140.12994030.11157656X-RAY DIFFRACTION92.93
1.14-1.150.13484110.10887808X-RAY DIFFRACTION93.99
1.15-1.170.14994140.11267861X-RAY DIFFRACTION94.44
1.17-1.180.14064130.11057845X-RAY DIFFRACTION94.85
1.18-1.20.13674160.11367904X-RAY DIFFRACTION95.13
1.2-1.220.13784150.11227895X-RAY DIFFRACTION95.3
1.22-1.240.13654140.11197864X-RAY DIFFRACTION95.13
1.24-1.260.13184200.11057980X-RAY DIFFRACTION95.53
1.26-1.280.12924190.11017957X-RAY DIFFRACTION96
1.28-1.30.13114230.11218027X-RAY DIFFRACTION96.31
1.3-1.330.12874200.10947990X-RAY DIFFRACTION96.19
1.33-1.360.1344210.11358001X-RAY DIFFRACTION96.34
1.36-1.390.14594220.11558012X-RAY DIFFRACTION96.32
1.39-1.420.144210.11367995X-RAY DIFFRACTION95.9
1.42-1.450.14114240.11748064X-RAY DIFFRACTION96.55
1.45-1.490.13534250.11438073X-RAY DIFFRACTION96.99
1.49-1.540.13414270.11138110X-RAY DIFFRACTION97.03
1.54-1.590.1294270.11268110X-RAY DIFFRACTION97.14
1.59-1.640.13114280.1148138X-RAY DIFFRACTION97.2
1.64-1.710.14414270.12268112X-RAY DIFFRACTION97.08
1.71-1.790.13324260.12698101X-RAY DIFFRACTION96.49
1.79-1.880.14654310.13898184X-RAY DIFFRACTION97.8
1.88-20.15334320.14288216X-RAY DIFFRACTION97.75
2-2.150.14574330.14288210X-RAY DIFFRACTION97.47
2.15-2.370.14784330.14878227X-RAY DIFFRACTION97.1
2.37-2.710.17814330.16238227X-RAY DIFFRACTION97.14
2.71-3.420.17484410.17078398X-RAY DIFFRACTION98.13
3.42-42.790.15714530.15818603X-RAY DIFFRACTION97.37

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