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- PDB-4f60: Crystal structure of Rhodococcus rhodochrous haloalkane dehalogen... -

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Basic information

Entry
Database: PDB / ID: 4f60
TitleCrystal structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant (T148L, G171Q, A172V, C176F).
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / mutation in access tunnel
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
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
FLUORIDE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPlevaka, M. / 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
Revision 1.2Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)34,2852
Polymers34,2661
Non-polymers191
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.018, 69.930, 85.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloalkane dehalogenase


Mass: 34266.082 Da / Num. of mol.: 1 / Mutation: T148L, G171Q, A172V, C176F
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-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BisTris propane pH6.5, 0.2M Sodium Fluoride,20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: 1.45→50 Å / Num. all: 56080 / Num. obs: 53781 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 65.84
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.2 / % possible all: 74.2

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Processing

Software
NameVersionClassification
MarDBdata collection
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FBW

3fbw


Resolution: 1.45→29.02 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.908 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17109 2721 5.1 %RANDOM
Rwork0.15 ---
all0.15108 53223 --
obs0.15108 50998 95.82 %-
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: 28.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 1 500 2843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9593396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43823.607122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63615380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8961517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021969
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21257
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21694
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.216
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.51515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0922426
X-RAY DIFFRACTIONr_scbond_it1.74531093
X-RAY DIFFRACTIONr_scangle_it2.6774.5962
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 160 -
Rwork0.179 2698 -
obs--70.05 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
12.6288-0.5244-0.318811.2964-0.77192.04330.0418-0.1039-0.0812-0.09830.0120.6348-0.0036-0.1254-0.0538-0.0788-0.00030.0354-0.1010.0188-0.0672-33.1649.35320.73
21.60330.25910.0171.5604-0.65851.52420.0178-0.0575-0.1649-0.0074-0.0208-0.0930.18220.12920.003-0.01940.00860.0146-0.11420.0215-0.082-19.906-3.53720.679
30.86890.01890.09731.4702-0.06570.9275-0.0083-0.0333-0.06210.0134-0.00660.04640.0812-0.00180.0149-0.0892-0.00150.009-0.13910.0117-0.1464-22.346.61716.293
41.23091.1906-1.15193.0422-0.18612.4858-0.0061-0.2332-0.10740.2624-0.0585-0.29510.16980.37640.0647-0.02420.0336-0.0581-0.01750.0473-0.0925-7.8966.08127.429
51.0477-0.1493-0.18631.2256-0.26551.2563-0.0508-0.037-0.1129-0.0479-0.0333-0.09440.18060.10380.0842-0.08780.02030.017-0.11810.0174-0.1142-11.2236.31711.337
62.10532.14240.698211.19435.20932.72860.08820.21730.4557-0.18490.1603-0.4129-0.40530.1341-0.2485-0.0251-0.03650.0286-0.02120.0008-0.0025-5.34226.18813.753
71.6955-0.0015-0.05191.4413-0.08041.3810.0104-0.20260.22360.26180.0177-0.1509-0.14440.1476-0.0281-0.0106-0.0073-0.0337-0.0623-0.0499-0.0667-13.57126.35928.068
80.53021.5854-1.16898.4467-5.46614.58640.0698-0.33020.11640.4274-0.03480.3444-0.08720.146-0.0349-0.05090.00810.039-0.0745-0.019-0.0573-31.3622.1223.957
93.24850.17971.78351.42530.53273.44110.0179-0.2488-0.11050.27750.03970.08560.15680.0049-0.05770.02070.00390.0333-0.06730.0121-0.1266-24.04713.03232.433
101.35870.3363-2.01292.2809-0.86175.14110.0628-0.18780.10590.20240.0449-0.1857-0.10.3345-0.1077-0.0640.004-0.0572-0.0268-0.0195-0.0921-7.39218.35227.224
111.9296-0.4088-0.51650.7620.21890.8128-0.0107-0.02610.0889-0.0398-0.0004-0.1384-0.01810.13970.0111-0.1001-0.00360.0118-0.11040.0243-0.1115-8.76917.5798.328
128.1211-7.553-5.68219.84213.09298.61180.1447-0.15850.4769-0.22040.1888-0.6798-0.54480.2047-0.3335-0.0658-0.02760.0346-0.07980.0233-0.0357-14.09426.6895.265
133.9023-2.7244-1.91593.05811.19771.37890.12670.3840.3406-0.2355-0.1423-0.3126-0.1311-0.06780.0155-0.05380.00750.0099-0.05070.0441-0.0837-16.87919.5420.247
140.77850.0696-0.18611.44960.6091.64710.00340.00040.06170.0242-0.04170.10770.0162-0.10570.0384-0.11370.0090.0007-0.13650.003-0.135-26.34317.60610.959
1516.3442-0.24251.086812.76711.38515.1974-0.09440.7079-0.3691-0.82540.1603-0.24510.27860.1265-0.0659-0.05-0.00260.0145-0.0766-0.0386-0.1183-21.7026.645-0.735
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 10
2X-RAY DIFFRACTION2A11 - 32
3X-RAY DIFFRACTION3A33 - 70
4X-RAY DIFFRACTION4A71 - 87
5X-RAY DIFFRACTION5A88 - 132
6X-RAY DIFFRACTION6A133 - 137
7X-RAY DIFFRACTION7A138 - 177
8X-RAY DIFFRACTION8A178 - 183
9X-RAY DIFFRACTION9A184 - 197
10X-RAY DIFFRACTION10A198 - 214
11X-RAY DIFFRACTION11A215 - 246
12X-RAY DIFFRACTION12A247 - 255
13X-RAY DIFFRACTION13A256 - 267
14X-RAY DIFFRACTION14A268 - 288
15X-RAY DIFFRACTION15A289 - 293

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