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- PDB-1yox: Structure of the conserved Protein of Unknown Function PA3696 fro... -

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Basic information

Entry
Database: PDB / ID: 1yox
TitleStructure of the conserved Protein of Unknown Function PA3696 from Pseudomonas aeruginosa
Componentshypothetical protein PA3696
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homologyMitochondrial biogenesis protein AIM24 / Mitochondrial biogenesis AIM24 superfamily / Mitochondrial biogenesis AIM24 / Double-stranded beta-helix / Mitochondrial biogenesis AIM24 / Tryptophan RNA-binding attenuator protein-like domain superfamily / 4-Layer Sandwich / Alpha Beta / TIGR00266 family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWalker, J.R. / Xu, X. / Gu, J. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray structure of the conserved hypothetical protein PA3696
Authors: Walker, J.R. / Xu, X. / Gu, J. / Savchenko, A.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 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 1.4Oct 30, 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: hypothetical protein PA3696
B: hypothetical protein PA3696
C: hypothetical protein PA3696
D: hypothetical protein PA3696
E: hypothetical protein PA3696
F: hypothetical protein PA3696


Theoretical massNumber of molelcules
Total (without water)162,3096
Polymers162,3096
Non-polymers00
Water4,234235
1
A: hypothetical protein PA3696
B: hypothetical protein PA3696
C: hypothetical protein PA3696


Theoretical massNumber of molelcules
Total (without water)81,1553
Polymers81,1553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-49 kcal/mol
Surface area23080 Å2
MethodPISA
2
D: hypothetical protein PA3696
E: hypothetical protein PA3696
F: hypothetical protein PA3696


Theoretical massNumber of molelcules
Total (without water)81,1553
Polymers81,1553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-56 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.912, 124.912, 164.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). THE EXPECTED BIOLOGICAL UNIT CONSISTS OF A TRIMER, OF WHICH 2 COPIES ARE FOUND IN THE ASYMMETRIC UNIT: CHAINS A,B,C AND CHAINS D,E,F.

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Components

#1: Protein
hypothetical protein PA3696


Mass: 27051.543 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3696 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.53 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 0.5M MgCl2, 0.1M Tris pH 8.5, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98043,0.98027,0.96517
DetectorType: SBC-3 / Detector: CCD / Date: Oct 26, 2004
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980431
20.980271
30.965171
ReflectionResolution: 2.3→50 Å / Num. obs: 58292 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.03
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.93 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.642 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27896 2952 5.1 %RANDOM
Rwork0.22455 ---
obs0.22732 55340 99.68 %-
all-55340 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8958 0 0 235 9193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.95912282
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97551159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6323.382414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.807151470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1441569
X-RAY DIFFRACTIONr_chiral_restr0.1120.21387
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026897
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.24005
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26023
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2487
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0421.55892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69729101
X-RAY DIFFRACTIONr_scbond_it2.34233598
X-RAY DIFFRACTIONr_scangle_it3.4494.53181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 212 -
Rwork0.258 3998 -
obs--99.98 %

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