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- PDB-2o6u: Crystal structure of the PA5185 protein from Pseudomonas Aerugino... -

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Basic information

Entry
Database: PDB / ID: 2o6u
TitleCrystal structure of the PA5185 protein from Pseudomonas Aeruginosa strain PAO1- new crystal form.
ComponentsTHIOESTERASE
KeywordsHYDROLASE / putative thioesterase / hot-dog fold
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
Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsChruszcz, M. / Koclega, K.D. / Evdokimova, E. / Cymborowski, M. / Kudritska, M. / Savchenko, A. / Edwards, A. / Minor, W.
CitationJournal: Cryst.Growth Des. / Year: 2008
Title: Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.
Authors: Chruszcz, M. / Zimmerman, M.D. / Wang, S. / Koclega, K.D. / Zheng, H. / Evdokimova, E. / Kudritska, M. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionDec 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOESTERASE
B: THIOESTERASE


Theoretical massNumber of molelcules
Total (without water)33,3522
Polymers33,3522
Non-polymers00
Water19811
1
A: THIOESTERASE
B: THIOESTERASE

A: THIOESTERASE
B: THIOESTERASE


Theoretical massNumber of molelcules
Total (without water)66,7034
Polymers66,7034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area8850 Å2
ΔGint-44 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.099, 93.099, 85.734
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 6 - 144 / Label seq-ID: 8 - 146

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

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Components

#1: Protein THIOESTERASE


Mass: 16675.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5185 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HU04
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 10, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 8614 / Num. obs: 8614 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.072 / Net I/σ(I): 23.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.5 / Num. unique all: 846 / Rsym value: 0.428 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AV9

2av9


Resolution: 3.01→37.85 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.886 / SU B: 35.414 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFMAC 5.2.0019 AND COOT WERE USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.23843 408 4.7 %RANDOM
Rwork0.19471 ---
all0.19677 8203 --
obs0.19677 8203 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.228 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å20 Å2
2---0.23 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 3.01→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 0 11 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222187
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9352976
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0615276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.05523.396106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.61615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9881515
X-RAY DIFFRACTIONr_chiral_restr0.1450.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021723
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.2942
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21499
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.51417
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49622203
X-RAY DIFFRACTIONr_scbond_it2.0463885
X-RAY DIFFRACTIONr_scangle_it3.1424.5773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
556tight positional0.070.05
498medium positional0.390.5
556tight thermal0.110.5
498medium thermal0.752
LS refinement shellResolution: 3.01→3.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 31 -
Rwork0.238 614 -
obs--98.77 %
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)
13.60820.27520.45452.00290.2454.10530.0175-0.2840.3470.3059-0.31260.4989-0.2973-0.66210.29520.0699-0.00810.04180.2314-0.16340.1738-39.40146.679-6.362
22.17590.1237-0.60083.8155-1.27014.2073-0.21550.00480.40450.13720.15040.3074-0.3063-0.29920.06510.12990.0493-0.0467-0.04580.00640.133-53.66613.45514.055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1448 - 146
2X-RAY DIFFRACTION2BB6 - 1448 - 146

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