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- PDB-3he1: Secreted protein Hcp3 from Pseudomonas aeruginosa. -

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Basic information

Entry
Database: PDB / ID: 3he1
TitleSecreted protein Hcp3 from Pseudomonas aeruginosa.
ComponentsMajor exported Hcp3 protein
Keywordsstructural genomics / unknown function / APC22128 / Hcp3 / HcpC / secretion / virulence / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Secreted
Function / homologyHcp1-like / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / extracellular region / Mainly Beta / Major exported protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.098 Å
AuthorsOsipiuk, J. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2011
Title: Crystal structure of secretory protein Hcp3 from Pseudomonas aeruginosa.
Authors: Osipiuk, J. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major exported Hcp3 protein
B: Major exported Hcp3 protein
C: Major exported Hcp3 protein
D: Major exported Hcp3 protein
E: Major exported Hcp3 protein
F: Major exported Hcp3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2118
Polymers132,0276
Non-polymers1842
Water13,115728
1
A: Major exported Hcp3 protein
B: Major exported Hcp3 protein

A: Major exported Hcp3 protein
B: Major exported Hcp3 protein

A: Major exported Hcp3 protein
B: Major exported Hcp3 protein


Theoretical massNumber of molelcules
Total (without water)132,0276
Polymers132,0276
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area14140 Å2
ΔGint-96 kcal/mol
Surface area32160 Å2
MethodPISA
2
C: Major exported Hcp3 protein
D: Major exported Hcp3 protein
hetero molecules

C: Major exported Hcp3 protein
D: Major exported Hcp3 protein
hetero molecules

C: Major exported Hcp3 protein
D: Major exported Hcp3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3039
Polymers132,0276
Non-polymers2763
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 area14720 Å2
ΔGint-99 kcal/mol
Surface area32030 Å2
MethodPISA
3
E: Major exported Hcp3 protein
F: Major exported Hcp3 protein
hetero molecules

E: Major exported Hcp3 protein
F: Major exported Hcp3 protein
hetero molecules

E: Major exported Hcp3 protein
F: Major exported Hcp3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3039
Polymers132,0276
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area14500 Å2
ΔGint-91 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.219, 141.219, 105.052
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Detailshexamer formed by subunits A and B and their symmetry related molecules

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Components

#1: Protein
Major exported Hcp3 protein / Secreted protein hcp


Mass: 22004.506 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: hcpC, PA0263 / Plasmid: pET15b modified / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HI36
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris buffer, 3.2 M sodium chloride, chymotrypsin partial digestion in crystallization droplet, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 17, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -k,h+k,l / Fraction: 0.509
ReflectionResolution: 2.098→39.8 Å / Num. all: 69851 / Num. obs: 69851 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.12 / Χ2: 2.01 / Net I/σ(I): 28.392
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 4.09 / Num. unique all: 3473 / Χ2: 1.439 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.098→39.8 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.619 / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
Details: twinned crystal, twin fraction: 0.51, twin operator: -k,h+k,l. PHENIX program treats Friedel pairs as two separate reflections, which generate bigger number of reflections used in refinement ...Details: twinned crystal, twin fraction: 0.51, twin operator: -k,h+k,l. PHENIX program treats Friedel pairs as two separate reflections, which generate bigger number of reflections used in refinement than in data collection.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 6053 5.35 %RANDOM
Rwork0.214 ---
all0.216 69851 --
obs0.216 -82.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.392 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 108.24 Å2 / Biso mean: 32.74 Å2 / Biso min: 7.24 Å2
Baniso -1Baniso -2Baniso -3
1--4.398 Å20 Å20 Å2
2---4.398 Å2-0 Å2
3---8.573 Å2
Refinement stepCycle: LAST / Resolution: 2.098→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6909 0 12 728 7649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087138
X-RAY DIFFRACTIONf_angle_d1.1899704
X-RAY DIFFRACTIONf_chiral_restr0.0761110
X-RAY DIFFRACTIONf_plane_restr0.0041215
X-RAY DIFFRACTIONf_dihedral_angle_d17.7452478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.099-2.1350.3323080.2659766284
2.135-2.1740.3343140.25859456259
2.174-2.2150.3013320.25259116243
2.215-2.260.2993260.25160066332
2.26-2.310.3172970.25256065903
2.31-2.3630.273090.24358956204
2.363-2.4220.2743070.23456345941
2.422-2.4880.2732890.23856885977
2.488-2.5610.3133260.24654765802
2.561-2.6440.2412670.23455045771
2.644-2.7380.2882780.2353295607
2.738-2.8480.2722450.21854005645
2.848-2.9770.3082900.21950985388
2.977-3.1340.2372570.19149385195
3.134-3.3310.1982520.18247154967
3.331-3.5880.1832270.16145124739
3.588-3.9480.1892410.15548295070
3.948-4.5190.1632540.14248755129
4.519-5.6910.232830.17748845167
5.691-39.8520.4752660.38653565622

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