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- PDB-2o6t: Crystal structure of the PA5185 protein from Pseudomonas Aerugino... -

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Basic information

Entry
Database: PDB / ID: 2o6t
TitleCrystal structure of the PA5185 protein from Pseudomonas Aeruginosa strain PAO1- orthorhombic form (P2221).
ComponentsTHIOESTERASE
KeywordsHYDROLASE / putative thioesterase / hot-dog fold
Function / homologyThioesterase-like superfamily / fatty acyl-CoA hydrolase activity / Thioesterase superfamily / 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: 2.55 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 / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
C: THIOESTERASE
E: THIOESTERASE
G: THIOESTERASE
I: THIOESTERASE
K: THIOESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,19610
Polymers100,0556
Non-polymers1424
Water4,522251
1
A: THIOESTERASE
C: THIOESTERASE
hetero molecules

A: THIOESTERASE
C: THIOESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7746
Polymers66,7034
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9780 Å2
ΔGint-76 kcal/mol
Surface area22260 Å2
MethodPISA
2
E: THIOESTERASE
G: THIOESTERASE
hetero molecules

E: THIOESTERASE
G: THIOESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8458
Polymers66,7034
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area9690 Å2
ΔGint-100 kcal/mol
Surface area22210 Å2
MethodPISA
3
I: THIOESTERASE
K: THIOESTERASE
hetero molecules

I: THIOESTERASE
K: THIOESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7746
Polymers66,7034
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area9810 Å2
ΔGint-77 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.924, 97.083, 191.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K

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
1SERSERAA6 - 1458 - 147
2ALAALACB6 - 1468 - 148
3SERSEREC6 - 1448 - 146
4SERSERGD6 - 1458 - 147
5SERSERIE6 - 1448 - 146
6ALAALAKF6 - 1468 - 148

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Components

#1: Protein
THIOESTERASE


Mass: 16675.775 Da / Num. of mol.: 6
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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, O.1M Bis-Tris pH 5.5, 0.5% NDSB-201, 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: 2.55→50 Å / Num. all: 36563 / Num. obs: 36563 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.121 / Rsym value: 0.095 / Net I/σ(I): 16.5
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3515 / Rsym value: 0.429 / % possible all: 98.2

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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: 2.55→39.53 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.864 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.473 / ESU R Free: 0.289 / 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
Rfree0.24788 1811 5 %RANDOM
Rwork0.1801 ---
obs0.18341 34661 99.34 %-
all-34661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.251 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.55→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6704 0 4 251 6959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226868
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9419349
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5275857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.99322.982342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.108151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3651560
X-RAY DIFFRACTIONr_chiral_restr0.120.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025408
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.23032
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.24783
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2176
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.851.54376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43826858
X-RAY DIFFRACTIONr_scbond_it2.32732806
X-RAY DIFFRACTIONr_scangle_it3.7484.52490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1034 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.350.5
2Cmedium positional0.480.5
3Emedium positional0.380.5
4Gmedium positional0.370.5
5Imedium positional0.410.5
6Kmedium positional0.470.5
1Amedium thermal1.12
2Cmedium thermal1.062
3Emedium thermal0.962
4Gmedium thermal0.992
5Imedium thermal1.082
6Kmedium thermal1.032
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 117 -
Rwork0.248 2445 -
obs--97.71 %

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