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- PDB-2xt0: Dehalogenase DPpA from Plesiocystis pacifica SIR-I -

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Basic information

Entry
Database: PDB / ID: 2xt0
TitleDehalogenase DPpA from Plesiocystis pacifica SIR-I
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE / ALPHA-BETA HYDROLASE FOLD
Function / homology
Function and homology information


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, putative
Similarity search - Component
Biological speciesPLESIOCYSTIS PACIFICA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBogdanovic, X. / Palm, G.J. / Hinrichs, W.
Citation
Journal: Appl.Microbiol.Biotechnol. / Year: 2011
Title: Cloning, Functional Expression, Biochemical Characterization, and Structural Analysis of a Haloalkane Dehalogenase from Plesiocystis Pacifica Sir-1.
Authors: Hesseler, M. / Bogdanovic, X. / Hidalgo, A. / Berenguer, J. / Palm, G.J. / Hinrichs, W. / Bornscheuer, U.T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Putative Haloalkane Dehalogenase Dppa from Plesiocystis Pacifica Sir-I.
Authors: Bogdanovic, X. / Hesseler, M. / Palm, G.J. / Bornscheuer, U.T. / Hinrichs, W.
History
DepositionOct 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Derived calculations
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)33,0085
Polymers32,6241
Non-polymers3844
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HALOALKANE DEHALOGENASE
hetero molecules

A: HALOALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,01710
Polymers65,2482
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2630 Å2
ΔGint-114.5 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.262, 108.501, 67.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HALOALKANE DEHALOGENASE / DPPA DEHALOGENASE


Mass: 32624.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLESIOCYSTIS PACIFICA (bacteria) / Strain: SIR-I / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: A6G7B1, haloalkane dehalogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 1.8M (NH4)2SO4, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 4, 2009 / Details: OSMIC MULTILAYER OPTIC
RadiationMonochromator: OSMIC MULTILAYER OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→38.68 Å / Num. obs: 25613 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CrystalClearV.1.3.6data reduction
CrystalClearV.1.3.6data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDB

1edb


Resolution: 1.9→67.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.419 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE NUMBER OF UNIQUE REFLECTIONS FOR REFINEMENT IS 25826 AND FOR DATA PROCESSING 25613. THIS IS DUE TO A DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE NUMBER OF UNIQUE REFLECTIONS FOR REFINEMENT IS 25826 AND FOR DATA PROCESSING 25613. THIS IS DUE TO A DIFFERENT RESOLUTION USED FOR REFINEMENT (1.9 A) AND PROCESSING (1.95 A).
RfactorNum. reflection% reflectionSelection details
Rfree0.24801 1375 5.1 %RANDOM
Rwork0.21931 ---
obs0.22081 25826 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 20 260 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222399
X-RAY DIFFRACTIONr_bond_other_d0.0010.021649
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9733271
X-RAY DIFFRACTIONr_angle_other_deg1.08533983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32422.883111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97915354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.61520
X-RAY DIFFRACTIONr_chiral_restr0.1180.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
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_it1.0721.51487
X-RAY DIFFRACTIONr_mcbond_other0.3621.5599
X-RAY DIFFRACTIONr_mcangle_it1.63822389
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7293912
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0394.5880
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 84 -
Rwork0.456 1775 -
obs--91.71 %
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)
10.97130.41810.07541.2971-0.18121.83470.0066-0.0242-0.05370.0508-0.0321-0.08640.05250.14360.02550.08020.0023-0.00570.06920.00370.09840.497318.970551.5628
21.07210.28130.48090.5047-0.71061.5888-0.06970.05530.0413-0.00020.05590.0422-0.0647-0.07580.01370.11630.00970.00310.11750.00230.119530.107822.712141.815
31.5813-0.809-0.79123.45670.86111.78860.0694-0.0886-0.21790.1952-0.13760.3050.159-0.13690.06830.1347-0.0416-0.00240.135300.12527.168412.562660.9103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 164
2X-RAY DIFFRACTION2A165 - 226
3X-RAY DIFFRACTION3A227 - 297

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