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

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Basic information

Entry
Database: PDB / ID: 4bau
TitleStructure of a putative epoxide hydrolase t131d mutant from Pseudomonas aeruginosa, with bound MFA
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
fluoroacetic acid / Probable epoxide hydrolase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsSchmidberger, J.W. / Schnell, R. / Schneider, G.
CitationJournal: To be Published
Title: Structure of a Putative Epoxide Hydrolase T131D Mutant from Pseudomonas Aeruginosa, with Bound Mfa
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 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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

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Assembly

Deposited unit
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,09418
Polymers33,6301
Non-polymers1,46417
Water6,720373
1
A: PROBABLE EPOXIDE HYDROLASE
hetero molecules

A: PROBABLE EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,18936
Polymers67,2602
Non-polymers2,92934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8460 Å2
ΔGint-257.1 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.860, 83.860, 140.570
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-2200-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3FO2
#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.: 373 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCLONING AND CUTTING OF HIS TAG LEFT EXTRA N-TERMINAL SERINE. 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: STRUCTURE WAS ACTUALLY SOLVED BY REFINING AGAINST NATIVE PA2086 STRUCTURE USING REFMAC.
Crystal growpH: 8.5
Details: 0.1 M LI2SO4, 1.25M (NH4)2SO4, 0.1 M TRIS HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.04088
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 1.55→17.7 Å / Num. obs: 71161 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4B9A

4b9a


Resolution: 1.55→17.57 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.177 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17094 3590 5 %RANDOM
Rwork0.13735 ---
obs0.13908 67543 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.55→17.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 81 373 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022518
X-RAY DIFFRACTIONr_bond_other_d0.0020.021690
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9723439
X-RAY DIFFRACTIONr_angle_other_deg1.133.0014047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3125311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58422.283127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07715373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2411528
X-RAY DIFFRACTIONr_chiral_restr0.120.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212846
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02558
X-RAY DIFFRACTIONr_nbd_refined0.270.2948
X-RAY DIFFRACTIONr_nbd_other0.2370.21638
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21154
X-RAY DIFFRACTIONr_nbtor_other0.110.21077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1340.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.23
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_restr4.8734208
X-RAY DIFFRACTIONr_sphericity_free31.03599
X-RAY DIFFRACTIONr_sphericity_bonded10.88454426
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 237 -
Rwork0.251 4483 -
obs--94.93 %

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