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- PDB-2pl6: Monoclinic crystal structure of hydrophobin HFBII in presence of ... -

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Basic information

Entry
Database: PDB / ID: 2pl6
TitleMonoclinic crystal structure of hydrophobin HFBII in presence of a detergent
ComponentsHydrophobin-2
KeywordsSTRUCTURAL 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: 2.2 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: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrophobin-2
B: Hydrophobin-2
C: Hydrophobin-2
D: Hydrophobin-2
E: Hydrophobin-2
F: Hydrophobin-2
G: Hydrophobin-2
H: Hydrophobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,49511
Polymers57,6128
Non-polymers8833
Water9,386521
1
A: Hydrophobin-2


Theoretical massNumber of molelcules
Total (without water)7,2011
Polymers7,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydrophobin-2


Theoretical massNumber of molelcules
Total (without water)7,2011
Polymers7,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hydrophobin-2


Theoretical massNumber of molelcules
Total (without water)7,2011
Polymers7,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hydrophobin-2


Theoretical massNumber of molelcules
Total (without water)7,2011
Polymers7,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hydrophobin-2


Theoretical massNumber of molelcules
Total (without water)7,2011
Polymers7,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hydrophobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4962
Polymers7,2011
Non-polymers2941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Hydrophobin-2


Theoretical massNumber of molelcules
Total (without water)7,2011
Polymers7,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Hydrophobin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7903
Polymers7,2011
Non-polymers5892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.080, 66.410, 79.770
Angle α, β, γ (deg.)90.00, 99.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 7201.474 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / References: UniProt: P79073
#2: 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.: 3 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.48
Details: 0.1 M lithium sulphate, 20% polyethylene glycol (MW 2000), 0.1 M tris (pH 8.5), pH 8.48, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 2006
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 62820 / Num. obs: 61949 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.1 / Num. unique all: 19998 / % possible all: 98.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.81 Å
Translation2.5 Å19.81 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R2M

1r2m


Resolution: 2.2→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3099 4.9 %random
Rwork0.224 ---
obs-61949 98.8 %-
Solvent computationBsol: 58.363 Å2
Displacement parametersBiso mean: 33.302 Å2
Baniso -1Baniso -2Baniso -3
1-7.624 Å20 Å2-0.284 Å2
2---3.215 Å20 Å2
3----4.409 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 57 521 4611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.306
X-RAY DIFFRACTIONc_mcbond_it1.7911.5
X-RAY DIFFRACTIONc_scbond_it1.9512
X-RAY DIFFRACTIONc_mcangle_it3.1142
X-RAY DIFFRACTIONc_scangle_it2.9562.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:htg.paramCNS_TOPPAR:htg.top

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