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- PDB-6y7b: X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled w... -

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Basic information

Entry
Database: PDB / ID: 6y7b
TitleX-ray structure of the Haloalkane dehalogenase HaloTag7 labeled with a chloroalkane-carbopyronine fluorophore substrate
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE / HALO / TAG / HALOTAG7 / SELF-LABELING PROTEIN / FLUOROPHORE / CARBOPYRONINE
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
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
Chem-OEK / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTarnawski, M. / Johnsson, K. / Hiblot, J.
Citation
Journal: Biochemistry / Year: 2021
Title: Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag.
Authors: Wilhelm, J. / Kuhn, S. / Tarnawski, M. / Gotthard, G. / Tunnermann, J. / Tanzer, T. / Karpenko, J. / Mertes, N. / Xue, L. / Uhrig, U. / Reinstein, J. / Hiblot, J. / Johnsson, K.
#1: Journal: Biorxiv / Year: 2021
Title: Kinetic and structural characterization of the self-labeling protein tags HaloTag7, SNAP-tag and CLIP-tag
Authors: Wilhelm, J. / Kuhn, S. / Tarnawski, M. / Gotthard, G. / Tunnermann, J. / Tanzer, T. / Karpenko, J. / Mertes, N. / Xue, L. / Uhrig, U. / Reinstein, J. / Hiblot, J. / Johnsson, K.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / pdbx_database_proc / struct
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 2.1Nov 10, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
C: Haloalkane dehalogenase
D: Haloalkane dehalogenase
E: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,62315
Polymers166,1305
Non-polymers3,49410
Water00
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9253
Polymers33,2261
Non-polymers6992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9253
Polymers33,2261
Non-polymers6992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9253
Polymers33,2261
Non-polymers6992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9253
Polymers33,2261
Non-polymers6992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9253
Polymers33,2261
Non-polymers6992
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.270, 161.270, 124.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A'A3 - 295
121chain 'A'A303
231chain 'B'B3 - 295
241chain 'B'B303
351chain 'C'C3 - 295
361chain 'C'C303
471chain 'D'D3 - 295
481chain 'D'D303
591chain 'E'E3 - 295
5101chain 'E'E303

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Components

#1: Protein
Haloalkane dehalogenase


Mass: 33225.980 Da / Num. of mol.: 5
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-OEK / 4-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]-2-[3-(dimethylamino)-6-(dimethyl-$l^{4}-azanylidene)-10,10-dimethyl-anthracen-9-yl]benzoic acid


Mass: 663.266 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H49ClN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bicine pH 9.0, 1.7 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: 1.00006 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00006 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 34294 / % possible obs: 99.8 % / Redundancy: 6.75 % / Biso Wilson estimate: 48.48 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.196 / Net I/σ(I): 8.53
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 6.99 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3081 / CC1/2: 0.857 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292106996

Resolution: 3.1→49.31 Å / SU ML: 0.3948 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9163
RfactorNum. reflection% reflection
Rfree0.2594 1715 5 %
Rwork0.2074 --
obs0.21 34290 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.23 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11750 0 235 0 11985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004312390
X-RAY DIFFRACTIONf_angle_d0.787516955
X-RAY DIFFRACTIONf_chiral_restr0.05281770
X-RAY DIFFRACTIONf_plane_restr0.00612360
X-RAY DIFFRACTIONf_dihedral_angle_d14.98987340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.190.33481410.28222680X-RAY DIFFRACTION99.86
3.19-3.290.34121420.26452704X-RAY DIFFRACTION99.89
3.29-3.410.34821400.26422659X-RAY DIFFRACTION100
3.41-3.550.31641420.26172685X-RAY DIFFRACTION99.82
3.55-3.710.3131410.24472697X-RAY DIFFRACTION99.79
3.71-3.910.26561430.22542701X-RAY DIFFRACTION99.86
3.91-4.150.2531410.19812692X-RAY DIFFRACTION99.96
4.15-4.470.24711430.17892703X-RAY DIFFRACTION99.86
4.47-4.920.22491420.17222699X-RAY DIFFRACTION99.93
4.92-5.630.19761440.17782734X-RAY DIFFRACTION99.79
5.63-7.090.26081450.19592761X-RAY DIFFRACTION99.62
7.09-49.310.19291510.16532860X-RAY DIFFRACTION99.77

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