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- PDB-7pcw: X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-M175W LAB... -

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Basic information

Entry
Database: PDB / ID: 7pcw
TitleX-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-M175W LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE / HALO / TAG / HALOTAG7 / SELF-LABELING PROTEIN / FLUOROPHORE / TETRAMETHYLRHODAMINE
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
Chem-OEH / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTarnawski, M. / Frei, M. / Hiblot, J. / Johnsson, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Methods / Year: 2022
Title: Engineered HaloTag variants for fluorescence lifetime multiplexing.
Authors: Frei, M.S. / Tarnawski, M. / Roberti, M.J. / Koch, B. / Hiblot, J. / Johnsson, K.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)135,81512
Polymers133,1244
Non-polymers2,6918
Water2,252125
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9543
Polymers33,2811
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9543
Polymers33,2811
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9543
Polymers33,2811
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9543
Polymers33,2811
Non-polymers6732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.320, 76.560, 85.760
Angle α, β, γ (deg.)68.397, 79.806, 79.021
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Haloalkane dehalogenase


Mass: 33280.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: C35H43ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.98 Å3/Da / Density % sol: 37.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.0, 1.0 M lithium chloride, 22% (m/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 26, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 43477 / % possible obs: 95.6 % / Redundancy: 2.67 % / Biso Wilson estimate: 28.14 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.44
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5246 / CC1/2: 0.769 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y7A

6y7a


Resolution: 2.3→40.36 Å / SU ML: 0.2773 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.3785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 2174 5 %
Rwork0.1908 41297 -
obs0.1934 43471 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9406 0 180 125 9711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00239918
X-RAY DIFFRACTIONf_angle_d0.576113570
X-RAY DIFFRACTIONf_chiral_restr0.0451408
X-RAY DIFFRACTIONf_plane_restr0.00531904
X-RAY DIFFRACTIONf_dihedral_angle_d13.49593700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.27511370.22182614X-RAY DIFFRACTION96.02
2.35-2.40.281350.22472562X-RAY DIFFRACTION96.7
2.4-2.460.30341380.23132624X-RAY DIFFRACTION95.31
2.46-2.530.2731360.23412580X-RAY DIFFRACTION97
2.53-2.610.32661370.22922612X-RAY DIFFRACTION95.39
2.61-2.690.33981360.23372577X-RAY DIFFRACTION96.69
2.69-2.790.29871380.22562610X-RAY DIFFRACTION96.02
2.79-2.90.3071340.22132552X-RAY DIFFRACTION96.13
2.9-3.030.28531350.20672569X-RAY DIFFRACTION95.72
3.03-3.190.27511370.21472612X-RAY DIFFRACTION95.09
3.19-3.390.26621340.20132531X-RAY DIFFRACTION95.31
3.39-3.650.24371370.17642608X-RAY DIFFRACTION96.59
3.65-4.020.20981360.1692593X-RAY DIFFRACTION95.92
4.02-4.60.18611340.15352544X-RAY DIFFRACTION95.1
4.6-5.790.18371350.16942550X-RAY DIFFRACTION94.21
5.79-40.360.17181350.15332559X-RAY DIFFRACTION94.96

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