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- PDB-4kac: X-Ray Structure of the complex HaloTag2 with HALTS. Northeast Str... -

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Basic information

Entry
Database: PDB / ID: 4kac
TitleX-Ray Structure of the complex HaloTag2 with HALTS. Northeast Structural Genomics Consortium (NESG) Target OR150.
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
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-1Q9 / AMMONIUM ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.223 Å
AuthorsKuzin, A. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. ...Kuzin, A. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Kornhaber, G. / Montelione, G.T. / Crews, C.M. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR150
Authors: Kuzin, A. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Kornhaber, G. / Montelione, G.T. / Crews, ...Authors: Kuzin, A. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Kornhaber, G. / Montelione, G.T. / Crews, C.M. / Hunt, J.F. / Tong, L.
History
DepositionApr 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)70,8386
Polymers69,9712
Non-polymers8674
Water4,936274
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2332
Polymers34,9861
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6054
Polymers34,9861
Non-polymers6203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.846, 94.984, 73.587
Angle α, β, γ (deg.)90.00, 93.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34985.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-1Q9 / N-(2-ethoxy-3,5-dimethylbenzyl)-1H-tetrazol-5-amine


Mass: 247.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N5O
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 277 K / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: ammonium nitrate 0.1M, sodium acetate 0.1M, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.223→50 Å / Num. obs: 51681 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.01 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BN7

1bn7


Resolution: 2.223→42.782 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.28 / σ(F): 1.89 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 1456 5.07 %
Rwork0.1746 --
obs0.178 28743 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.625 Å2
Refinement stepCycle: LAST / Resolution: 2.223→42.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 50 274 4996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084910
X-RAY DIFFRACTIONf_angle_d1.1636708
X-RAY DIFFRACTIONf_dihedral_angle_d14.1271806
X-RAY DIFFRACTIONf_chiral_restr0.081700
X-RAY DIFFRACTIONf_plane_restr0.007880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2228-2.30220.31891500.19072591X-RAY DIFFRACTION95
2.3022-2.39440.24351330.18222744X-RAY DIFFRACTION99
2.3944-2.50330.32191380.18022718X-RAY DIFFRACTION99
2.5033-2.63530.27251600.18122706X-RAY DIFFRACTION99
2.6353-2.80040.26741430.18812729X-RAY DIFFRACTION99
2.8004-3.01650.2461430.18782729X-RAY DIFFRACTION100
3.0165-3.320.27661390.18572775X-RAY DIFFRACTION100
3.32-3.80020.21771530.17462734X-RAY DIFFRACTION100
3.8002-4.78680.2041370.14742777X-RAY DIFFRACTION100
4.7868-42.78950.19871600.1652784X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.0749 Å / Origin y: 11.0063 Å / Origin z: 20.6503 Å
111213212223313233
T0.0999 Å2-0.009 Å2-0.0091 Å2-0.1057 Å20.0153 Å2--0.1286 Å2
L0.1544 °2-0.1125 °2-0.2151 °2-0.2979 °20.3831 °2--0.6525 °2
S-0.0097 Å °0.0054 Å °0.0064 Å °-0.0008 Å °-0.0276 Å °0.0248 Å °-0.0067 Å °-0.0343 Å °0.0424 Å °
Refinement TLS groupSelection details: all

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