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- PDB-5uy1: X-ray crystal structure of apo Halotag -

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Basic information

Entry
Database: PDB / ID: 5uy1
TitleX-ray crystal structure of apo Halotag
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / fluorogenic / halo / tag
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
Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 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 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)69,18510
Polymers68,7682
Non-polymers4178
Water7,873437
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6065
Polymers34,3841
Non-polymers2224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5795
Polymers34,3841
Non-polymers1954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.077, 94.628, 99.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34384.199 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.24 % / Mosaicity: 0.237 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: NaCl, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 144106 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Χ2: 0.905 / Net I/σ(I): 8 / Num. measured all: 1023559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.376.70.79370880.7920.3250.8590.75399.5
1.37-1.46.80.69471250.8330.2840.7510.76499.8
1.4-1.436.80.61170880.8680.2490.6610.76799.9
1.43-1.456.80.53671570.890.2180.580.77599.9
1.45-1.496.90.44771300.9240.1810.4830.793100
1.49-1.526.90.38871570.9410.1580.4190.814100
1.52-1.5670.32971370.9540.1330.3550.83699.9
1.56-1.670.2871630.9650.1130.3020.87599.9
1.6-1.6570.24271450.9720.0980.2610.92100
1.65-1.77.10.20871690.9780.0840.2250.965100
1.7-1.767.10.17271820.9850.0690.1850.987100
1.76-1.837.20.1471750.9890.0560.1511.004100
1.83-1.927.20.11271880.9930.0450.120.986100
1.92-2.027.30.0972100.9950.0360.0971.078100
2.02-2.147.40.0772220.9970.0280.0751.014100
2.14-2.317.40.06272400.9970.0250.0671.134100
2.31-2.547.50.05372510.9980.0210.0571.081100
2.54-2.917.50.0472900.9990.0160.0430.891100
2.91-3.667.40.02873690.9990.0110.030.778100
3.66-507.10.02676200.9990.0110.0280.81699.7

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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: 1.35→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.853 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.053
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 7029 5 %RANDOM
Rwork0.1881 ---
obs0.1885 133179 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 45.86 Å2 / Biso mean: 14.426 Å2 / Biso min: 9.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0 Å2
2--0.02 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 23 437 5116
Biso mean--24.21 23.6 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194841
X-RAY DIFFRACTIONr_bond_other_d0.0010.024558
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9596613
X-RAY DIFFRACTIONr_angle_other_deg0.74310499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6845582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75223.333228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40615737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1071534
X-RAY DIFFRACTIONr_chiral_restr0.0570.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021120
LS refinement shellResolution: 1.348→1.383 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 390 -
Rwork0.238 7030 -
all-7420 -
obs--70.18 %

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