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- PDB-2pl7: Orhorhombic crystal structure of hydrophobin HFBII in the presenc... -

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Basic information

Entry
Database: PDB / ID: 2pl7
TitleOrhorhombic crystal structure of hydrophobin HFBII in the presence of a detergent
ComponentsHydrophobin-2
KeywordsSURFACE ACTIVE PROTEIN / hydrophobin / amphiphile / protein surfactant
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 speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsKallio, J.M. / Rouvinen, J.P.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structures of Hydrophobin HFBII in the Presence of Detergent Implicate the Formation of Fibrils and Monolayer Films.
Authors: Kallio, J.M. / Linder, M.B. / Rouvinen, J.
History
DepositionApr 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,7934
Polymers14,4032
Non-polymers3902
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.300, 57.100, 72.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) Hypocrea jecorina (fungus) / References: UniProt: P79073
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.92 Å3/Da / Density % sol: 31.918 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.91
Details: 0.1 M lithium sulphate, 20% polyethylene glycol (MW2000), 0.1M Tris (pH 8.5), pH 6.91, 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: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2006
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→20 Å / Num. all: 109088 / Num. obs: 107245 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 8.243 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.82
Reflection shellResolution: 1→1.2 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.9 / Num. measured obs: 104770 / Num. unique all: 44537 / % possible all: 96.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å19.51 Å
Translation4 Å19.51 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
SHELXrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R2M

1r2m


Resolution: 1→20 Å / Num. parameters: 10287 / Num. restraintsaints: 12647 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1515 2832 5.3 %RANDOM
obs0.1796 107245 98.3 %-
all-109088 --
Displacement parametersBiso mean: 10.2 Å2
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 948 / Occupancy sum non hydrogen: 1073.52
Refinement stepCycle: LAST / Resolution: 1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 29 149 1141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0338
X-RAY DIFFRACTIONs_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.115
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.069
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.084

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