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- PDB-4bat: Structure of a putative epoxide hydrolase t131d mutant from Pseud... -

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Basic information

Entry
Database: PDB / ID: 4bat
TitleStructure of a putative epoxide hydrolase t131d mutant from Pseudomonas aeruginosa.
ComponentsPROBABLE EPOXIDE HYDROLASE
KeywordsHYDROLASE
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
Probable epoxide hydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSchmidberger, J.W. / Schnell, R. / Schneider, G.
CitationJournal: To be Published
Title: Structure of a Putative Epoxide Hydrolase T131D Mutant from Pseudomonas Aeruginosa.
Authors: Schmidberger, J.W. / Schnell, R. / Schneider, G.
History
DepositionSep 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 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

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Assembly

Deposited unit
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,61812
Polymers33,6301
Non-polymers98811
Water8,323462
1
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules

A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23624
Polymers67,2602
Non-polymers1,97622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5880 Å2
ΔGint-211.3 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.880, 83.880, 140.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2275-

HOH

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Components

#1: Protein PROBABLE EPOXIDE HYDROLASE / PA2086


Mass: 33629.965 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9I229
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLONING AND CUTTING OF THE HIS TAG LEAVES AND EXTRA N- TERMINAL SERINE. THIS STRUCTURE IS A T131D MUTANT.

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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: 3.67 Å3/Da / Density % sol: 66.5 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M LI2SO4, 1.25 M (NH4)2SO4, 0.1 M TRISCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→72.06 Å / Num. obs: 123442 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.8
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B9A

4b9a


Resolution: 1.3→23.37 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.046 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.14268 6193 5 %RANDOM
Rwork0.12163 ---
obs0.12269 117206 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å20 Å2
2--0.11 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 53 462 2850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192544
X-RAY DIFFRACTIONr_bond_other_d0.0010.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9693486
X-RAY DIFFRACTIONr_angle_other_deg0.99934168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1865323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06222.093129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35915386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9471530
X-RAY DIFFRACTIONr_chiral_restr0.1070.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
X-RAY DIFFRACTIONr_nbd_refined0.2750.21073
X-RAY DIFFRACTIONr_nbd_other0.2330.21639
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21176
X-RAY DIFFRACTIONr_nbtor_other0.1090.21091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1590.27
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.277
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.69234276
X-RAY DIFFRACTIONr_sphericity_free42.6645112
X-RAY DIFFRACTIONr_sphericity_bonded11.28554558
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 427 -
Rwork0.297 8043 -
obs--100 %

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