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- PDB-1yll: Crystal Structure of the Conserved Protein of Unknown Function PA... -

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Basic information

Entry
Database: PDB / ID: 1yll
TitleCrystal Structure of the Conserved Protein of Unknown Function PA5104 from Pseudomonas aeruginosa PAO1
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / beta-barrels / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyUncharacterised protein family HutD/Ves / HutD / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / HutD family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å
AuthorsMidwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Conserved Hypothetical Protein PA5104 from Pseudomonas aeruginosa PAO1
Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Savchenko, A. / Edwards, A.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 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 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
D: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)87,4934
Polymers87,4934
Non-polymers00
Water13,926773
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.514, 67.209, 82.768
Angle α, β, γ (deg.)90.00, 111.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
conserved hypothetical protein / PA5104


Mass: 21873.234 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): BL21DE3 / References: UniProt: Q9HU79
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, magnesium chloride, Tris, L-lysine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.9794, 0.956
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
30.9561
ReflectionResolution: 1.64→77.15 Å / Num. all: 84910 / Num. obs: 82845 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.4
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.7 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.64→77.15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24328 8261 10 %RANDOM
Rwork0.19409 ---
obs0.19906 74054 96.07 %-
all-74055 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.1 Å2
2--0.83 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.64→77.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5912 0 0 773 6685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.948600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4215816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98222.263327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.814151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3241583
X-RAY DIFFRACTIONr_chiral_restr0.1310.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025085
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.5240.23164
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24133
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2615
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.2117
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7741.53930
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.00926218
X-RAY DIFFRACTIONr_scbond_it2.96132403
X-RAY DIFFRACTIONr_scangle_it4.2454.52382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.641→1.683 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 541
Rwork0.299 4508

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