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- PDB-2o5u: Crystal structure of the PA5185 protein from Pseudomonas Aerugino... -

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Basic information

Entry
Database: PDB / ID: 2o5u
TitleCrystal structure of the PA5185 protein from Pseudomonas Aeruginosa strain PAO1- orthorhombic form (C222).
ComponentsThioesterase
KeywordsHYDROLASE / putative thioesterese
Function / homology: / Thioesterase-like superfamily / fatty acyl-CoA hydrolase activity / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsChruszcz, M. / Wang, S. / Evdokimova, E. / Koclega, K.D. / 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 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
A: Thioesterase
B: Thioesterase
C: Thioesterase


Theoretical massNumber of molelcules
Total (without water)49,6553
Polymers49,6553
Non-polymers00
Water4,936274
1
A: Thioesterase
B: Thioesterase

A: Thioesterase
B: Thioesterase


Theoretical massNumber of molelcules
Total (without water)66,2074
Polymers66,2074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area9580 Å2
ΔGint-45 kcal/mol
Surface area21200 Å2
MethodPISA, PQS
2
C: Thioesterase

C: Thioesterase

C: Thioesterase

C: Thioesterase


Theoretical massNumber of molelcules
Total (without water)66,2074
Polymers66,2074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)124.039, 148.157, 58.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11C-156-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLNGLNAA6 - 1437 - 144
2SERSERBB6 - 1447 - 145
3SERSERCC6 - 1447 - 145

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Components

#1: Protein Thioesterase


Mass: 16551.654 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HU04
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 20% PEG 3350, 0.1M Bis-Tris, 0.05M MES, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41694 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.091 / Rsym value: 0.069 / Net I/σ(I): 17.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3678 / Rsym value: 0.393 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AV9

2av9


Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.938 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22296 2103 5 %RANDOM
Rwork0.19059 ---
all0.19225 39591 --
obs0.19225 39591 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 0 274 3589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223420
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9414660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.195430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71623.529170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12415507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1731525
X-RAY DIFFRACTIONr_chiral_restr0.1270.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022695
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21571
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22391
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1451.52195
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75823425
X-RAY DIFFRACTIONr_scbond_it2.80831396
X-RAY DIFFRACTIONr_scangle_it4.1884.51233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1036 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.30.5
2Bmedium positional0.330.5
3Cmedium positional0.340.5
1Amedium thermal1.282
2Bmedium thermal1.522
3Cmedium thermal1.382
LS refinement shellResolution: 1.91→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 141 -
Rwork0.23 2443 -
obs--83.17 %

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