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- PDB-4wcv: Haloalkane dehalogenase DhaA mutant from Rhodococcus rhodochrous ... -

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Basic information

Entry
Database: PDB / ID: 4wcv
TitleHaloalkane dehalogenase DhaA mutant from Rhodococcus rhodochrous (T148L+G171Q+A172V+C176G)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / mutation in tunnel access
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
ACETATE ION / TRIETHYLENE GLYCOL / Haloalkane dehalogenase / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHolubeva, T. / Prudnikova, T. / Kuta-Smatanova, I. / Rezacova, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicP207/12/0775 Czech Republic
CitationJournal: Chemcatchem / Year: 2015
Title: Balancing the stability-activity trade-off by fine-tuning dehalogenase access tunnels
Authors: Liskova, V. / Bednar, D. / Prudnikova, T. / Rezacova, P. / Koudelakova, T. / Sebestova, E. / Kuta-Smatanova, I. / Brezovsky, J. / Chaloupkova, R. / Damborsky, J.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4805
Polymers34,1761
Non-polymers3044
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-11 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.585, 44.477, 46.508
Angle α, β, γ (deg.)115.47, 98.79, 109.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 34175.961 Da / Num. of mol.: 1 / Mutation: T148L+G171Q+A172V+C176G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A3G3, UniProt: P0A3G2*PLUS, 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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: sodium acetate trihydrate, ammonium acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.69→39.42 Å / Num. all: 30835 / Num. obs: 28416 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.76
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.16 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G9X

3g9x


Resolution: 1.69→39.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.179 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17573 1421 5 %RANDOM
Rwork0.12015 ---
obs0.12295 26995 92.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20.01 Å2
2--0.03 Å20.01 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.69→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 19 477 2861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9593510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9223.566129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81215386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5481518
X-RAY DIFFRACTIONr_chiral_restr0.1370.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0222061
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1030.6951210
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4081520
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2440.7981347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.4494567
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.11232531
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded10.69652436
LS refinement shellResolution: 1.689→1.733 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 99 -
Rwork0.114 1882 -
obs--87.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.0941-0.0263-0.04140.07280.01270.08770.00250.0065-0.0028-0.0024-0.00380.0099-0.0005-0.00770.00130.0146-0.0075-0.01070.00490.0050.0088Chain A 4-132 residua-5.0761.49-6.656
20.25450.36810.34360.53930.49130.4698-0.02650.0105-0.0039-0.05170.0252-0.0091-0.02760.01020.00140.026-0.00770.00560.01780.00180.013Chain A 133-144 residua6.512-8.96714.484
30.23-0.3543-0.23840.59150.35450.2655-0.0149-0.0132-0.00220.02690.00720.00780.00850.00870.00770.0197-0.0032-0.00970.01740.00280.0106Chain A 145-158 residua-0.35-0.46420.143
40.8467-0.3209-0.43560.15870.13360.2509-0.0062-0.0330.02310.00350.0105-0.0195-0.00110.0173-0.00420.0179-0.005-0.00640.00790.00350.007Chain A 159-167 residua-5.2899.03818.027
50.3429-0.1738-0.07340.14390.10660.1033-0.007-0.01590.01540.00290.0106-0.0113-0.00420.0087-0.00370.0175-0.0101-0.01210.00890.00250.0163Chain A 168-185 residua7.29711.6447.67
60.45480.0982-0.45380.6742-0.03860.51090.01550.02450.03140.00910.00820.0147-0.0104-0.0065-0.02370.0195-0.0041-0.00980.00940.00760.01Chain A 186-196 residua-3.29815.6275.73
70.059-0.0146-0.04730.29710.04860.0915-0.0010.0034-0.0120.0065-0.00810.01810.0056-0.00210.00920.0159-0.0074-0.00990.00680.00630.0123Chain A 197-230 residua-4.793-7.6337.796
80.01170.04710.01320.32660.11810.1324-0.0048-0.0065-0.00260.0150.007-0.00610.02270.0092-0.00220.020.001-0.00790.01750.0070.0126Chain A 231-263 residua11.4-11.143-1.972
90.12780.0108-0.0120.08740.10340.23710.0053-0.0047-0.006-0.00770.0028-0.0151-0.00370.0081-0.00810.0167-0.006-0.00940.00490.0050.0117Chain A 264-295 residua11.201-0.574-7.994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 132
2X-RAY DIFFRACTION2A133 - 144
3X-RAY DIFFRACTION3A145 - 158
4X-RAY DIFFRACTION4A159 - 167
5X-RAY DIFFRACTION5A168 - 185
6X-RAY DIFFRACTION6A186 - 196
7X-RAY DIFFRACTION7A197 - 230
8X-RAY DIFFRACTION8A231 - 263
9X-RAY DIFFRACTION9A264 - 295

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