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- PDB-4f5z: Crystal structure of Rhodococcus rhodochrous haloalkane dehalogen... -

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Basic information

Entry
Database: PDB / ID: 4f5z
TitleCrystal structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant (L95V, A172V).
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / mutation in access tunnel
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
BENZOIC ACID / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsKulik, D. / Kuta-Smatanova, I. / Rezacova, P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel.
Authors: Koudelakova, T. / Chaloupkova, R. / Brezovsky, J. / Prokop, Z. / Sebestova, E. / Hesseler, M. / Khabiri, M. / Plevaka, M. / Kulik, D. / Kuta Smatanova, I. / Rezacova, P. / Ettrich, R. / ...Authors: Koudelakova, T. / Chaloupkova, R. / Brezovsky, J. / Prokop, Z. / Sebestova, E. / Hesseler, M. / Khabiri, M. / Plevaka, M. / Kulik, D. / Kuta Smatanova, I. / Rezacova, P. / Ettrich, R. / Bornscheuer, U.T. / Damborsky, J.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2823
Polymers34,1251
Non-polymers1582
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.663, 44.489, 46.389
Angle α, β, γ (deg.)115.28, 98.61, 109.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 34124.895 Da / Num. of mol.: 1 / Mutation: L95V, A172V
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(DE3) / References: UniProt: P0A3G2, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35 % (w/v) PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 18, 2012
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 78455 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 18.85
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2.5 / % possible all: 72.1

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Processing

Software
NameVersionClassification
MarDBdata collection
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3FBW
Resolution: 1.2→17.17 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.065 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15495 3937 5 %RANDOM
Rwork0.12007 ---
all0.12185 ---
obs0.12185 74518 91.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20.17 Å2
2--0.23 Å20.19 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.2→17.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 10 745 3105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222586
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9633578
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80323.651126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09415394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.441517
X-RAY DIFFRACTIONr_chiral_restr0.10.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022081
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21388
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.21767
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2567
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.2102
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2961.51574
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81922555
X-RAY DIFFRACTIONr_scbond_it2.5731145
X-RAY DIFFRACTIONr_scangle_it3.3654.51004
X-RAY DIFFRACTIONr_rigid_bond_restr1.77732719
X-RAY DIFFRACTIONr_sphericity_free5.6593746
X-RAY DIFFRACTIONr_sphericity_bonded4.20832478
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 209 -
Rwork0.155 4150 -
obs--69.16 %

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