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- PDB-4kaf: Crystal Structure of Haloalkane dehalogenase HaloTag7 at the reso... -

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Basic information

Entry
Database: PDB / ID: 4kaf
TitleCrystal Structure of Haloalkane dehalogenase HaloTag7 at the resolution 1.5A, Northeast Structural Genomics Consortium (NESG) Target OR151
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


haloalkane dehalogenase activity / haloalkane dehalogenase / 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
DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.496 Å
AuthorsKuzin, A.P. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. ...Kuzin, A.P. / 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. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR151
Authors: Kuzin, A.P. / 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. / Tong, L.
History
DepositionApr 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release

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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)71,13013
Polymers70,6462
Non-polymers48411
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.930, 94.800, 100.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer,35.49 kD,99.1%

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Haloalkane dehalogenase /


Mass: 35322.859 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

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Non-polymers , 5 types, 697 molecules

#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 277 K / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: ammonium thiocynate, MES 0.1M, PEG 4000 20%, 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 5, 2012
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: 1.496→50 Å / Num. obs: 203311 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 9.83 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 36.6

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E46
Resolution: 1.496→44.399 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.09 / σ(F): 1.34 / Phase error: 14.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1649 3857 1.9 %
Rwork0.1483 --
obs0.1486 203210 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.171 Å2-0 Å20 Å2
2--0.2 Å20 Å2
3----0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.496→44.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4764 0 27 686 5477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095035
X-RAY DIFFRACTIONf_angle_d1.3646883
X-RAY DIFFRACTIONf_dihedral_angle_d12.1341858
X-RAY DIFFRACTIONf_chiral_restr0.079727
X-RAY DIFFRACTIONf_plane_restr0.008909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.496-1.51420.2246980.19395975X-RAY DIFFRACTION83
1.5142-1.53340.19171460.18416875X-RAY DIFFRACTION95
1.5334-1.55360.15421600.16847152X-RAY DIFFRACTION99
1.5536-1.57490.18151260.1617104X-RAY DIFFRACTION99
1.5749-1.59740.20371110.15427148X-RAY DIFFRACTION99
1.5974-1.62120.16281620.1527084X-RAY DIFFRACTION99
1.6212-1.64660.13471370.14877190X-RAY DIFFRACTION99
1.6466-1.67360.16921520.15097151X-RAY DIFFRACTION100
1.6736-1.70240.15251250.14827133X-RAY DIFFRACTION99
1.7024-1.73340.18061390.15167164X-RAY DIFFRACTION100
1.7334-1.76670.16861360.1467199X-RAY DIFFRACTION100
1.7667-1.80280.14771300.13927178X-RAY DIFFRACTION100
1.8028-1.8420.15971470.13887162X-RAY DIFFRACTION100
1.842-1.88480.16591420.13857172X-RAY DIFFRACTION100
1.8848-1.9320.12661190.13837225X-RAY DIFFRACTION100
1.932-1.98420.15821540.14187168X-RAY DIFFRACTION100
1.9842-2.04260.14761320.13817173X-RAY DIFFRACTION100
2.0426-2.10850.1851510.1417205X-RAY DIFFRACTION100
2.1085-2.18390.15491280.14067168X-RAY DIFFRACTION100
2.1839-2.27130.16651450.14137207X-RAY DIFFRACTION100
2.2713-2.37470.15261420.1377227X-RAY DIFFRACTION100
2.3747-2.49990.14581360.13647182X-RAY DIFFRACTION100
2.4999-2.65650.16681360.14417208X-RAY DIFFRACTION100
2.6565-2.86150.13911470.14397183X-RAY DIFFRACTION100
2.8615-3.14940.15051400.15267197X-RAY DIFFRACTION100
3.1494-3.6050.19021330.14987190X-RAY DIFFRACTION100
3.605-4.54120.17721370.14247197X-RAY DIFFRACTION100
4.5412-44.41860.18951460.18067136X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.1329 Å / Origin y: -31.3022 Å / Origin z: 25.4694 Å
111213212223313233
T0.0616 Å20.0017 Å2-0.0056 Å2-0.0493 Å2-0.0009 Å2--0.0775 Å2
L0.2038 °20.0192 °2-0.115 °2-0.1399 °20.0004 °2--0.4888 °2
S-0.0096 Å °-0.0018 Å °-0.0114 Å °-0.0015 Å °0.0038 Å °0.0021 Å °0.0181 Å °0.0017 Å °0.0077 Å °
Refinement TLS groupSelection details: all

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