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- PDB-1y12: Structure of a hemolysin-coregulated protein from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 1y12
TitleStructure of a hemolysin-coregulated protein from Pseudomonas aeruginosa
Componentshypothetical protein PA0085
Keywordsstructural genomics / unknown function / Pseudomonas aeruginosa / hemolysin-corregulation / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


extracellular region / identical protein binding
Similarity search - Function
Hcp1-like / : / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsCuff, M.E. / Zhou, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Science / Year: 2006
Title: A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus.
Authors: Mougous, J.D. / Cuff, M.E. / Raunser, S. / Shen, A. / Zhou, M. / Gifford, C.A. / Goodman, A.L. / Joachimiak, G. / Ordonez, C.L. / Lory, S. / Walz, T. / Joachimiak, A. / Mekalanos, J.J.
History
DepositionNov 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 22, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Mar 11, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] ..._pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PA0085
B: hypothetical protein PA0085
C: hypothetical protein PA0085


Theoretical massNumber of molelcules
Total (without water)53,9653
Polymers53,9653
Non-polymers00
Water9,674537
1
A: hypothetical protein PA0085
C: hypothetical protein PA0085

A: hypothetical protein PA0085
C: hypothetical protein PA0085

A: hypothetical protein PA0085
C: hypothetical protein PA0085


Theoretical massNumber of molelcules
Total (without water)107,9306
Polymers107,9306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area16160 Å2
ΔGint-146 kcal/mol
Surface area40350 Å2
MethodPISA
2
B: hypothetical protein PA0085
x 6


Theoretical massNumber of molelcules
Total (without water)107,9306
Polymers107,9306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area16480 Å2
ΔGint-148 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.729, 146.729, 42.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

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Components

#1: Protein hypothetical protein PA0085


Mass: 17988.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: PA0085 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9I747
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, HEPES, tri-sodium citrate, Peritone N, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943, 0.97956, 0.96863
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979431
20.979561
30.968631
ReflectionResolution: 1.95→48.03 Å / Num. all: 37749 / Num. obs: 37749 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.04 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
HKL-2000data scaling
SOLVEphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.13 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22665 1919 5.1 %RANDOM
Rwork0.1794 ---
all0.18174 35832 --
obs0.18174 35832 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 0 537 4146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223667
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9454935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9125472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.82926.154156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49815660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.257159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022728
X-RAY DIFFRACTIONr_nbd_refined0.1770.21555
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22493
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2452
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.259
X-RAY DIFFRACTIONr_mcbond_it0.7411.52416
X-RAY DIFFRACTIONr_mcangle_it1.00623723
X-RAY DIFFRACTIONr_scbond_it1.69531458
X-RAY DIFFRACTIONr_scangle_it2.5694.51212
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 143 -
Rwork0.237 2341 -
obs--88.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.18290.12640.30881.1762-0.45141.49270.0287-0.0040.1238-0.1243-0.02770.26570.06580.0708-0.001-0.03790.0372-0.0263-0.0486-0.02560.025846.52154.19432.548
21.47570.2950.15890.36890.15211.21110.0124-0.06830.0546-0.04430.00060.03050.0359-0.0509-0.0130.0072-0.0167-0.0109-0.02160.0053-0.078520.79120.75613.443
30.80670.81270.39620.83240.2731.3661-0.03320.01130.0388-0.0695-0.01590.0317-0.05360.0950.0491-0.03560.0032-0.0067-0.0135-0.0164-0.037249.53925.26132.22
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1625 - 165
2X-RAY DIFFRACTION2BB2 - 1625 - 165
3X-RAY DIFFRACTION3CC2 - 1625 - 165

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