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- PDB-3qy3: PA2801 protein, a putative Thioesterase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3qy3
TitlePA2801 protein, a putative Thioesterase from Pseudomonas aeruginosa
ComponentsThioesterase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
: / Thioesterase-like superfamily / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Acyl-CoA thioesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsOsipiuk, J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Biochem.J. / Year: 2012
Title: Structure and activity of the Pseudomonas aeruginosa hotdog-fold thioesterases PA5202 and PA2801.
Authors: Gonzalez, C.F. / Tchigvintsev, A. / Brown, G. / Flick, R. / Evdokimova, E. / Xu, X. / Osipiuk, J. / Cuff, M.E. / Lynch, S. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionMar 16, 2011ID: 2ALI
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8882
Polymers17,8521
Non-polymers351
Water1,856103
1
A: Thioesterase
hetero molecules

A: Thioesterase
hetero molecules

A: Thioesterase
hetero molecules

A: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5528
Polymers71,4104
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area7840 Å2
ΔGint-69 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.816, 58.907, 85.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

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Components

#1: Protein Thioesterase


Mass: 17852.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2801 / Plasmid: PET15B modified / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I042
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M CALCIUM CHLORIDE, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2005
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97951
ReflectionResolution: 1.75→39.7 Å / Num. all: 13809 / Num. obs: 13809 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 47.7
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.9 / Num. unique all: 854 / % possible all: 79.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→39.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.704 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1375 10 %RANDOM
Rwork0.1653 ---
all0.1694 13809 --
obs0.1694 13809 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.8 Å2 / Biso mean: 32.3292 Å2 / Biso min: 9.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--1.13 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 1 103 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211104
X-RAY DIFFRACTIONr_bond_other_d0.0010.02719
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9371523
X-RAY DIFFRACTIONr_angle_other_deg0.9431759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18922.88552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99215171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.722158
X-RAY DIFFRACTIONr_chiral_restr0.1150.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
X-RAY DIFFRACTIONr_mcbond_it1.0561.5670
X-RAY DIFFRACTIONr_mcbond_other0.3321.5270
X-RAY DIFFRACTIONr_mcangle_it1.86621094
X-RAY DIFFRACTIONr_scbond_it2.8433434
X-RAY DIFFRACTIONr_scangle_it4.434.5421
LS refinement shellResolution: 1.749→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 68 -
Rwork0.337 744 -
all-812 -
obs-812 79.61 %
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)
11.17490.59540.17331.21490.61940.7579-0.0508-0.1406-0.01030.00330.0255-0.01670.0110.02340.02530.08530.0087-0.0070.11170.00290.06237.8055-0.85479.0495
21.6108-0.32780.63321.0664-0.66791.7661-0.1264-0.15540.17840.00440.0593-0.1499-0.3041-0.04530.06710.13750.0174-0.03610.0575-0.04330.072213.298510.27377.0842
32.65711.4376-0.34182.23680.05870.8729-0.0104-0.3274-0.0210.07070.048-0.17690.04290.0965-0.03760.06970.0181-0.01610.0967-0.020.065815.96770.717311.6824
41.20320.4-0.22581.8231-0.66551.57730.0157-0.2987-0.03190.1303-0.049-0.2069-0.10110.11660.03330.1024-0.0046-0.01990.0972-0.01880.070216.93671.165911.2616
54.70590.32595.97523.82-3.235327.8129-0.6436-0.15780.732-0.40920.1491-0.2088-0.99840.14540.49450.2351-0.0388-0.03840.0359-0.06050.161919.803321.20698.0897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 42
2X-RAY DIFFRACTION2A43 - 66
3X-RAY DIFFRACTION3A67 - 90
4X-RAY DIFFRACTION4A91 - 116
5X-RAY DIFFRACTION5A117 - 134

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