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- PDB-1yre: Hypothetical protein PA3270 from Pseudomonas aeruginosa in comple... -

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Basic information

Entry
Database: PDB / ID: 1yre
TitleHypothetical protein PA3270 from Pseudomonas aeruginosa in complex with CoA
Componentshypothetical protein PA3270Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC5563 / PA3270 / Midwest Center for Structural Genomics / MSCG / Protein Structure Initiative / PSI / MCSG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / : / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsLunin, V.V. / Osipiuk, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of hypothetical protein PA3270 from Pseudomonas aeruginosa in complex with CoA
Authors: Lunin, V.V. / Skarina, T. / Osipiuk, J. / Joachimiak, A. / Edwards, A.M. / Savchenko, A.
History
DepositionFeb 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: hypothetical protein PA3270
B: hypothetical protein PA3270
C: hypothetical protein PA3270
D: hypothetical protein PA3270
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5728
Polymers88,5024
Non-polymers3,0704
Water7,710428
1
A: hypothetical protein PA3270
B: hypothetical protein PA3270
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7864
Polymers44,2512
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-2 kcal/mol
Surface area16670 Å2
MethodPISA
2
C: hypothetical protein PA3270
D: hypothetical protein PA3270
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7864
Polymers44,2512
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.590, 92.053, 105.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer. The asymmetric unit contains two dimers (chains A.B) and (chains C,D)

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Components

#1: Protein
hypothetical protein PA3270 / Hypothesis


Mass: 22125.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: MODIFIED PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: GenBank: 9949395, UniProt: Q9HYX1*PLUS
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M NaCl, 0.1M TrisHCl, 25%PEG3350, 1mM AcCoA, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.97906 / Wavelength: 0.97906 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 43452 / Num. obs: 43452 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.075 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.16 / Num. unique all: 7890 / Rsym value: 0.576 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALAdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.778 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26451 2083 5.1 %RANDOM
Rwork0.2011 ---
all0.20441 38538 --
obs0.20441 38538 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.333 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2---1.03 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 192 428 6468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216177
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8942.0028403
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3255737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91822.621290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.317151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7071572
X-RAY DIFFRACTIONr_chiral_restr0.1220.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024654
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.22782
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24039
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2450
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6231.53837
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78225878
X-RAY DIFFRACTIONr_scbond_it3.29732705
X-RAY DIFFRACTIONr_scangle_it5.0324.52525
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 144 -
Rwork0.234 2680 -
obs--94.35 %

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