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- PDB-4wdr: Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+... -

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Basic information

Entry
Database: PDB / ID: 4wdr
TitleCrystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86) from Sphingobium japonicum UT26
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Protein Engineering / Tertiary / Sphingobioum
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / periplasmic space
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
Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingobium japonicum UT26S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsDegtjarik, O. / Rezacova, P. / Iermak, I. / Chaloupkova, R. / Damborsky, J. / Kuta-Smatanova, I.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Academy of SciencesRVO 61388963 Czech Republic
Czech Academy of SciencesRVO 68378050 Czech Republic
Czech Science FoundationP207/12/0775 Czech Republic
CitationJournal: Acs Catalysis / Year: 2016
Title: Crystal structure of haloalkane dehalogenase LinB mutant (L177W) from Sphingobium japonicum UT26
Authors: Degtjarik, O. / Rezacova, P. / Chaloupkova, R. / Damborsky, J. / Kuta-Smatanova, I.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_symm_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2
Revision 2.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)65,5855
Polymers65,4742
Non-polymers1113
Water1,09961
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8133
Polymers32,7371
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7732
Polymers32,7371
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.937, 125.937, 213.818
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-302-

CA

21B-402-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 4 - 294 / Label seq-ID: 1 - 291

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Haloalkane dehalogenase


Mass: 32737.082 Da / Num. of mol.: 2 / Fragment: UNP residues 4-296 / Mutation: W140A, F143L, L177W, I211L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium japonicum UT26S (bacteria) / Gene: linB, dhaA, SJA_C1-19590 / Production host: Escherichia coli (E. coli) / References: UniProt: D4Z2G1, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M MOPS, 0.1M HEPES; 0.3M MgCl2; 0.3M CaCl2; 20% PEG550MME; 10%PEG20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972386 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 23, 2013
RadiationMonochromator: Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972386 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 22938 / Num. obs: 22874 / % possible obs: 99.7 % / Redundancy: 7.81 % / Net I/σ(I): 14.66
Reflection shellResolution: 2.5→2.65 Å / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.14 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.476
Highest resolutionLowest resolution
Rotation48.58 Å3.03 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
MOLREP11.1.03phasing
PDB_EXTRACT3.14data extraction
Cootmodel building
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WDQ

4wdq


Resolution: 2.5→48.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1745 / WRfactor Rwork: 0.1471 / FOM work R set: 0.8512 / SU B: 19.081 / SU ML: 0.19 / SU R Cruickshank DPI: 0.5208 / SU Rfree: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.521 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1144 5 %RANDOM
Rwork0.1651 21730 --
obs0.1667 -99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.53 Å2 / Biso mean: 59.36 Å2 / Biso min: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å2-0 Å2
2--0.18 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 2.5→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 3 61 4673
Biso mean--66.26 47.28 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194733
X-RAY DIFFRACTIONr_bond_other_d0.0050.024435
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.956427
X-RAY DIFFRACTIONr_angle_other_deg1.058310177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8275583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7722.821234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83715740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4751550
X-RAY DIFFRACTIONr_chiral_restr0.0910.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215393
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021129
X-RAY DIFFRACTIONr_mcbond_it2.0182.9762338
X-RAY DIFFRACTIONr_mcbond_other2.0182.9772337
X-RAY DIFFRACTIONr_mcangle_it3.0234.472919
Refine LS restraints NCS

Ens-ID: 1 / Number: 18036 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.498→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 81 -
Rwork0.351 1549 -
all-1630 -
obs--97.37 %
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)
16.1545-4.902811.20714.3741-9.922322.52510.28210.9580.4805-0.2173-0.8871-0.27090.49292.05910.6050.36690.12430.00980.5599-0.03080.648510.87925.85750.361
21.4058-0.4753-0.33212.33970.55731.3902-0.0444-0.19790.11910.18480.0461-0.3150.09010.1934-0.00160.05240.0353-0.06330.1157-0.00460.1419-1.17923.63154.474
31.0457-0.40190.16761.95250.43060.77260.01450.0277-0.0596-0.1622-0.0083-0.10780.03560.0024-0.00620.10040.00050.00310.07960.00980.0808-9.61219.98642.38
41.1731-0.4252-0.56352.78120.00161.8958-0.03760.09450.2596-0.17670.0732-0.1455-0.1269-0.0641-0.03570.12830.0267-0.00490.09890.00780.1049-11.02837.29845.836
53.4899-0.90670.04831.84690.43050.31690.3976-0.0087-1.1513-0.0062-0.16470.00750.3363-0.3272-0.23280.7072-0.3721-0.2650.57650.04190.9857-36.8526.17279.859
60.88611.5009-0.81734.608-1.6726.26710.2412-0.1544-0.30540.6687-0.04680.1267-0.1528-0.7953-0.19440.4419-0.3137-0.08060.62160.04060.703-41.50717.83385.118
72.08290.06490.80681.53470.10540.73950.33840.0655-0.61320.0673-0.09760.00710.2559-0.2174-0.24070.2595-0.1118-0.07520.2315-0.04890.3356-26.53619.53578.074
81.69522.8065-3.468111.5151-3.6698.2410.2204-0.4533-0.61440.4201-0.8097-0.7657-0.07050.81570.58930.7838-0.0985-0.35280.48660.23351.4259-20.391.56287.449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 13
2X-RAY DIFFRACTION2A14 - 108
3X-RAY DIFFRACTION3A109 - 224
4X-RAY DIFFRACTION4A225 - 296
5X-RAY DIFFRACTION5B4 - 71
6X-RAY DIFFRACTION6B72 - 101
7X-RAY DIFFRACTION7B102 - 279
8X-RAY DIFFRACTION8B280 - 295

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