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- PDB-2ijc: Structure of a Conserved Protein of Unknown Function PA0269 from ... -

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Basic information

Entry
Database: PDB / ID: 2ijc
TitleStructure of a Conserved Protein of Unknown Function PA0269 from Pseudomonas aeruginosa
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / hypothetical protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsBinkowski, T.A. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a Conserved Hypothetical Protein PA0269 from Pseudomonas aeruginosa
Authors: Binkowski, T.A. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 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
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
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 9 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 9 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
E: Hypothetical protein
F: Hypothetical protein
G: Hypothetical protein
H: Hypothetical protein
I: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)148,0959
Polymers148,0959
Non-polymers00
Water15,006833
1
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
E: Hypothetical protein
F: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)98,7306
Polymers98,7306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-103 kcal/mol
Surface area31270 Å2
MethodPISA
2
G: Hypothetical protein
H: Hypothetical protein
I: Hypothetical protein

G: Hypothetical protein
H: Hypothetical protein
I: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)98,7306
Polymers98,7306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)183.507, 76.719, 109.011
Angle α, β, γ (deg.)90.00, 119.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hypothetical protein / Conserved Hypothetical Protein PA0269


Mass: 16454.965 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: PA0269 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6M1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 7, 2005
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 83801 / Num. obs: 77091 / % possible obs: 92.2211 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.05→2.1 Å / % possible all: 82.46

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→34.59 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.974 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.233 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 4076 5 %RANDOM
Rwork0.19024 ---
all0.234 ---
obs0.19346 77091 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.409 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å2-0.14 Å2
2---1.89 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10054 0 0 833 10887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.95713913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.56951275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99123.717487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.956151730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0791590
X-RAY DIFFRACTIONr_chiral_restr0.1750.21521
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027849
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.25478
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.27020
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2836
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3820.264
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8781.56640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.415210113
X-RAY DIFFRACTIONr_scbond_it2.28734285
X-RAY DIFFRACTIONr_scangle_it3.424.53800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 281 -
Rwork0.234 4806 -
obs--82.46 %

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