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- PDB-6u32: Crystal structure of HaloTag bound to tetramethylrhodamine-HaloTa... -

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Basic information

Entry
Database: PDB / ID: 6u32
TitleCrystal structure of HaloTag bound to tetramethylrhodamine-HaloTag ligand
ComponentsHaloTag
KeywordsHYDROLASE / HaloTag / Haloalkane dehalogenase / tetramethyrhodamine
Function / homologyChem-PVY
Function and homology information
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBerro, A.J. / Schreiter, E.R.
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: The HaloTag as a general scaffold for far-red tunable chemigenetic indicators.
Authors: Deo, C. / Abdelfattah, A.S. / Bhargava, H.K. / Berro, A.J. / Falco, N. / Farrants, H. / Moeyaert, B. / Chupanova, M. / Lavis, L.D. / Schreiter, E.R.
History
DepositionAug 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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 / 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: HaloTag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2833
Polymers33,6441
Non-polymers6382
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.530, 62.530, 164.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HaloTag


Mass: 33644.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PVY / 9-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-6-(dimethylamino)-N,N-dimethyl-3H-xanthen-3-iminium


Mass: 602.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H44N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M MgCl2, 0.1M Tris pH 8.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→58.435 Å / Num. all: 30022 / Num. obs: 30022 / % possible obs: 97 % / Redundancy: 5.8 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.108 / Rsym value: 0.098 / Net I/av σ(I): 6.1 / Net I/σ(I): 11.2 / Num. measured all: 174075
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.95.90.9770.72555743190.4311.0710.9772.497.6
1.9-2.015.60.5691.22249140020.2580.6270.5693.695.5
2.01-2.156.10.4311.52364538930.1860.4710.4315.398.2
2.15-2.325.70.2263.12060536050.1010.2490.2267.697.5
2.32-2.555.80.1534.61903032730.0680.1680.1539.896.3
2.55-2.855.90.1086.51824030750.0480.1180.1081398.5
2.85-3.295.60.0689.31489926650.0310.0750.06818.496.1
3.29-4.0260.05411.61391023340.0240.0590.05426.498.5
4.02-5.695.50.04413.9999418030.0210.0490.04428.995.7
5.69-62.535.40.03516570410530.0160.0390.03527.394.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UY1

5uy1


Resolution: 1.8→58.43 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.1506 / FOM work R set: 0.8527 / SU B: 5.637 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1109 / SU Rfree: 0.1084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 1545 5.2 %RANDOM
Rwork0.1573 ---
obs0.1592 28449 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.23 Å2 / Biso mean: 28.574 Å2 / Biso min: 15.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.23 Å2
Refinement stepCycle: final / Resolution: 1.8→58.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 77 177 2599
Biso mean--36.26 36.4 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192514
X-RAY DIFFRACTIONr_bond_other_d0.0050.022293
X-RAY DIFFRACTIONr_angle_refined_deg2.5371.9863440
X-RAY DIFFRACTIONr_angle_other_deg1.3663.0065307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69723.448116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52415371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7791517
X-RAY DIFFRACTIONr_chiral_restr0.1550.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 101 -
Rwork0.245 2084 -
all-2185 -
obs--96.72 %
Refinement TLS params.Method: refined / Origin x: 86.862 Å / Origin y: 59.99 Å / Origin z: 10.573 Å
111213212223313233
T0.1376 Å20.0158 Å20.0127 Å2-0.0524 Å20.0146 Å2--0.006 Å2
L1.1208 °20.2896 °20.3302 °2-0.7338 °20.2352 °2--2.4658 °2
S-0.0136 Å °0.0319 Å °0.0111 Å °0.0923 Å °0.0069 Å °0.0211 Å °0.2362 Å °0.1386 Å °0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 295
2X-RAY DIFFRACTION1A301

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