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- PDB-5uxz: X-ray crystal structure of Halotag bound to the P9 benzothiadiazo... -

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Basic information

Entry
Database: PDB / ID: 5uxz
TitleX-ray crystal structure of Halotag bound to the P9 benzothiadiazole fluorogenic ligand
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / fluorogenic / halo / tag / solvatochromatic
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-8PM / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.92 Å
AuthorsDunham, N.P. / Boal, A.K.
CitationJournal: Biochemistry / Year: 2017
Title: The Cation-pi Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification.
Authors: Liu, Y. / Miao, K. / Dunham, N.P. / Liu, H. / Fares, M. / Boal, A.K. / Li, X. / Zhang, X.
History
DepositionFeb 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,7908
Polymers69,7682
Non-polymers1,0226
Water1,29772
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4575
Polymers34,8841
Non-polymers5734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3333
Polymers34,8841
Non-polymers4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.939, 69.124, 83.904
Angle α, β, γ (deg.)90.000, 94.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34883.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-8PM / N~2~-{[7-(dimethylamino)-2,1,3-benzothiadiazol-4-yl]sulfonyl}-N-hexyl-N~2~-methylglycinamide


Mass: 413.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N5O3S2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.55 % / Mosaicity: 0.289 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.6 / Details: PEG 4000, Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 42358 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.057 / Rrim(I) all: 0.11 / Χ2: 0.932 / Net I/σ(I): 11.7 / Num. measured all: 156567
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.92-1.953.20.51118100.7610.3210.6060.95484.9
1.95-1.993.30.43819020.8970.270.5160.91386.9
1.99-2.033.40.36719130.9230.2250.4310.89688.6
2.03-2.073.40.33719700.9360.2070.3970.93191
2.07-2.113.50.29720500.920.1810.3480.9595
2.11-2.163.60.27621530.9530.1680.3240.88498.1
2.16-2.223.70.23921270.9630.1430.2790.87899.2
2.22-2.283.80.22421840.9730.1330.2611.08999.9
2.28-2.343.80.20721620.9730.1220.241.157100
2.34-2.423.80.16621760.9780.0980.1940.899100
2.42-2.513.80.14121750.9840.0830.1640.883100
2.51-2.613.80.12421770.9760.0740.1450.898100
2.61-2.723.80.10621690.9860.0630.1230.843100
2.72-2.873.80.08121720.9890.0480.0950.702100
2.87-3.053.80.07222040.9910.0430.0840.701100
3.05-3.283.80.06921880.9890.0410.080.707100
3.28-3.613.80.07121750.9860.0420.0830.726100
3.61-4.143.80.06821920.9840.040.0790.747100
4.14-5.213.80.07622040.9750.0450.0890.855100
5.21-503.70.11622550.8980.0720.1372.04199.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.92→50 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.871 / SU B: 6.417 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1806 5.1 %RANDOM
Rwork0.2686 ---
obs0.2696 33903 81.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.07 Å2 / Biso mean: 25.852 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å20.29 Å2
2---0.93 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 64 72 4827
Biso mean--24.65 18.39 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194917
X-RAY DIFFRACTIONr_bond_other_d0.0010.024611
X-RAY DIFFRACTIONr_angle_refined_deg0.961.9726721
X-RAY DIFFRACTIONr_angle_other_deg0.716310633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6185583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04423.362229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84815743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4081534
X-RAY DIFFRACTIONr_chiral_restr0.0550.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021129
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 57 -
Rwork0.301 1270 -
all-1327 -
obs--41.69 %

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