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- PDB-6zcc: X-ray structure of the Haloalkane dehalogenase HOB (HaloTag7-base... -

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Basic information

Entry
Database: PDB / ID: 6zcc
TitleX-ray structure of the Haloalkane dehalogenase HOB (HaloTag7-based Oligonucleotide Binder) labeled with a chloroalkane-tetramethylrhodamine fluorophore substrate
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE / HALO / TAG / HALOTAG7 / SELF-LABELING PROTEIN / (SYNTHETIC) FLUOROPHORE / TETRAMETHYLRHODAMINE / OLIGONUCLEOTIDE BINDER
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-OEH / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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
DepositionJun 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Nov 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 1.3Jan 24, 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 1.4Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2697
Polymers33,4121
Non-polymers8576
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-22 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.210, 64.770, 78.850
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: 33412.410 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-OEH / [9-[2-carboxy-5-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium


Mass: 637.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H43ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium acetate, 20% (m/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99984 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 23, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38699 / % possible obs: 88.9 % / Redundancy: 5.91 % / Biso Wilson estimate: 24.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 18.87
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 2.38 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 3579 / CC1/2: 0.934 / % possible all: 47.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 1.52→43.53 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.4276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 1934 5 %
Rwork0.1887 36763 -
obs0.1905 38697 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.52→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 52 312 2699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00942479
X-RAY DIFFRACTIONf_angle_d1.01423385
X-RAY DIFFRACTIONf_chiral_restr0.0581351
X-RAY DIFFRACTIONf_plane_restr0.0077473
X-RAY DIFFRACTIONf_dihedral_angle_d6.11092046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.4412610.38221160X-RAY DIFFRACTION41.54
1.56-1.60.39061130.31242152X-RAY DIFFRACTION76.24
1.6-1.650.34571270.27322423X-RAY DIFFRACTION86.21
1.65-1.70.27991370.25682589X-RAY DIFFRACTION92.22
1.7-1.760.31831450.24642770X-RAY DIFFRACTION98.31
1.76-1.830.29591480.23632806X-RAY DIFFRACTION99.46
1.83-1.910.29251480.23822809X-RAY DIFFRACTION99.43
1.91-2.010.25951500.22292841X-RAY DIFFRACTION99.87
2.01-2.140.28511480.20782827X-RAY DIFFRACTION99.83
2.14-2.30.23951500.20272846X-RAY DIFFRACTION99.9
2.3-2.540.24691500.20212853X-RAY DIFFRACTION99.93
2.54-2.90.25461520.19592875X-RAY DIFFRACTION99.93
2.9-3.660.19871530.16682904X-RAY DIFFRACTION99.84
3.66-43.530.15871520.15262908X-RAY DIFFRACTION95.3

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