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- PDB-5vnp: X-ray crystal structure of Halotag bound to the P1 benzoxadiazole... -

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Basic information

Entry
Database: PDB / ID: 5vnp
TitleX-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / biosensor / cytotoxicity / fluorescent probe / protein aggregation / proteome stress
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-9FM / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsDunham, N.P. / Boal, A.K.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress.
Authors: Liu, Y. / Fares, M. / Dunham, N.P. / Gao, Z. / Miao, K. / Jiang, X. / Bollinger, S.S. / Boal, A.K. / Zhang, X.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)66,8676
Polymers65,8532
Non-polymers1,0144
Water1,45981
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4343
Polymers32,9271
Non-polymers5072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4343
Polymers32,9271
Non-polymers5072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.272, 69.481, 88.950
Angle α, β, γ (deg.)90.000, 95.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haloalkane dehalogenase


Mass: 32926.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-9FM / N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide


Mass: 471.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H33N5O6S
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 40.49 % / Mosaicity: 0.496 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: PEG 8000, Sodium Acetate, Sodium Cacodylate

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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: 2.23→50 Å / Num. obs: 26164 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.084 / Rrim(I) all: 0.164 / Χ2: 0.933 / Net I/σ(I): 5 / Num. measured all: 99216
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.23-2.293.70.6160.7770.3740.7221.008100
2.29-2.333.70.5670.7680.340.6620.91199.5
2.33-2.383.80.5230.7940.3130.610.89599.8
2.38-2.423.80.4830.8290.2870.5630.909100
2.42-2.483.80.4430.830.2620.5150.931100
2.48-2.533.80.4070.870.2410.4740.907100
2.53-2.63.80.3510.8850.2080.4080.924100
2.6-2.673.80.3420.8810.2030.3980.933100
2.67-2.753.80.2890.9360.1710.3360.947100
2.75-2.833.80.2460.9450.1460.2860.946100
2.83-2.943.80.2210.9520.1310.2570.936100
2.94-3.053.80.1830.9670.1090.2130.968100
3.05-3.193.80.150.9760.0890.1741100
3.19-3.363.80.1130.9850.0670.1320.931100
3.36-3.573.80.0990.9880.0590.1151.046100
3.57-3.853.80.0850.9880.0510.0991.131100
3.85-4.233.80.0620.9950.0370.0721.015100
4.23-4.853.80.0460.9970.0280.0540.85899.9
4.85-6.13.80.0450.9970.0270.0530.75100
6.1-503.60.0370.9980.0230.0440.69799.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UY1

5uy1


Resolution: 2.23→44 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.497 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.435 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1299 5.1 %RANDOM
Rwork0.1975 ---
obs0.1991 24385 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.74 Å2 / Biso mean: 27.863 Å2 / Biso min: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0.36 Å2
2---0.46 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.23→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 66 81 4803
Biso mean--44.39 26.97 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194884
X-RAY DIFFRACTIONr_bond_other_d0.0010.024578
X-RAY DIFFRACTIONr_angle_refined_deg0.9741.9726676
X-RAY DIFFRACTIONr_angle_other_deg0.73310556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4775578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.85623.333228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09915734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1641534
X-RAY DIFFRACTIONr_chiral_restr0.0550.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021126
LS refinement shellResolution: 2.227→2.284 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 71 -
Rwork0.261 1349 -
all-1420 -
obs--74.42 %

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