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- PDB-3qqt: Amphiphilic nanotubes in the crystal structure of a biosurfactant... -

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Basic information

Entry
Database: PDB / ID: 3qqt
TitleAmphiphilic nanotubes in the crystal structure of a biosurfactant protein hydrophobin HFBII
ComponentsHydrophobin-2
KeywordsSTRUCTURAL PROTEIN / Surface active protein / amphiphile
Function / homology
Function and homology information


spore wall / extracellular region
Similarity search - Function
Cerato-ulmin hydrophobin family / Fungal hydrophobin / hfbii hydrophobin / Hydrophobin / Hydrophobin superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKallio, J.M. / Rouvinen, J.
CitationJournal: Chem.Commun.(Camb.) / Year: 2011
Title: Amphiphilic nanotubes in the crystal structure of a biosurfactant protein hydrophobin HFBII.
Authors: Kallio, J.M. / Rouvinen, J.
History
DepositionFeb 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrophobin-2
B: Hydrophobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9586
Polymers14,4032
Non-polymers5554
Water1,65792
1
A: Hydrophobin-2
hetero molecules

A: Hydrophobin-2
hetero molecules

A: Hydrophobin-2
hetero molecules

A: Hydrophobin-2
hetero molecules

B: Hydrophobin-2
hetero molecules

B: Hydrophobin-2
hetero molecules

B: Hydrophobin-2
hetero molecules

B: Hydrophobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,83024
Polymers57,6128
Non-polymers2,21816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_665x+1,-y+1,-z1
Buried area10950 Å2
ΔGint-251 kcal/mol
Surface area25280 Å2
MethodPISA
2
A: Hydrophobin-2
B: Hydrophobin-2
hetero molecules

A: Hydrophobin-2
B: Hydrophobin-2
hetero molecules

A: Hydrophobin-2
B: Hydrophobin-2
hetero molecules

A: Hydrophobin-2
B: Hydrophobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,83024
Polymers57,6128
Non-polymers2,21816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11180 Å2
ΔGint-191 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.052, 91.359, 94.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-89-

HOH

21A-90-

HOH

31B-112-

HOH

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Components

#1: Protein Hydrophobin-2 / / Hydrophobin II / HFBII


Mass: 7201.474 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoderma reesei (fungus) / References: UniProt: P79073
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SDS / DODECYL SULFATE / Sodium dodecyl sulfate


Mass: 266.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O4S / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% polyethylene glycol MW 2000, 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5, Stock solution of polystyrene nanospheres, diameter 50 nm, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2007 / Details: mirrors
RadiationMonochromator: Double crystal Si(111), horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 27834 / Num. obs: 27376 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.089
Reflection shell
Resolution (Å)% possible all
1.9-2.296.4
2.2-2.599.3
2.5-2.899.6
2.8-399.9
3-499.8
4-599.9

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Processing

Software
NameVersionClassification
XDSpackagedata scaling
CCP4model building
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSpackagedata reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R2M

1r2m


Resolution: 1.9→19.22 Å / σ(F): 1.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 1391 5.08 %RANDOM
Rwork0.2112 ---
obs0.2138 14601 98.47 %-
all-27834 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.691 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3499 Å20 Å20 Å2
2--1.3333 Å2-0 Å2
3---1.0166 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 32 92 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071022
X-RAY DIFFRACTIONf_angle_d1.2271384
X-RAY DIFFRACTIONf_dihedral_angle_d18.34358
X-RAY DIFFRACTIONf_chiral_restr0.068176
X-RAY DIFFRACTIONf_plane_restr0.006172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97990.30651450.29022808X-RAY DIFFRACTION91
1.9799-2.06990.30251470.26392849X-RAY DIFFRACTION94
2.0699-2.17890.32811540.24962892X-RAY DIFFRACTION94
2.1789-2.31520.29291490.24962888X-RAY DIFFRACTION94
2.3152-2.49360.31081510.25462881X-RAY DIFFRACTION94
2.4936-2.74390.28091530.23982920X-RAY DIFFRACTION95
2.7439-3.13950.24941560.23472937X-RAY DIFFRACTION95
3.1395-3.94960.2271450.1752894X-RAY DIFFRACTION95
3.9496-19.10070.22181500.15222926X-RAY DIFFRACTION95

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