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- PDB-7s86: Crystal structure of hydrophobin SC16, C2221 -

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Basic information

Entry
Database: PDB / ID: 7s86
TitleCrystal structure of hydrophobin SC16, C2221
ComponentsHydrophobin
KeywordsSTRUCTURAL PROTEIN / hydrophobin / self-assembly / surface modifier
Function / homologyFungal hydrophobin / Hydrophobin, conserved site / Fungal hydrophobins signature. / Hydrophobin / Hydrophobins / structural constituent of cell wall / fungal-type cell wall / extracellular region / Hydrophobin
Function and homology information
Biological speciesSchizophyllum commune (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVergunst, K.L. / Langelaan, D.N.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: Sci Rep / Year: 2022
Title: The N-terminal tail of the hydrophobin SC16 is not required for rodlet formation
Authors: Vergunst, K.L. / Langelaan, D.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrophobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2464
Polymers10,0991
Non-polymers1473
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, Exists as a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint1 kcal/mol
Surface area5680 Å2
Unit cell
Length a, b, c (Å)49.180, 96.290, 37.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

21A-250-

HOH

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Components

#1: Protein Hydrophobin


Mass: 10098.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains a naturally occurring mutation compared to UniProt (insertion of Ser30 and Lys31).
Source: (gene. exp.) Schizophyllum commune (fungus) / Gene: HYD1, SCHCODRAFT_58269 / Production host: Escherichia coli (E. coli) / References: UniProt: D8QCG9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.01 Å3/Da / Density % sol: 44.59 % / Description: Large clusters of plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M Citric acid pH 3.5 30.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5408 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5408 Å / Relative weight: 1
ReflectionResolution: 2→43.8 Å / Num. obs: 6317 / % possible obs: 99.09 % / Redundancy: 11.5 % / Biso Wilson estimate: 32.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.016 / Rrim(I) all: 0.054 / Net I/σ(I): 29.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 596 / CC1/2: 0.994 / CC star: 0.998 / Rpim(I) all: 0.105 / Rrim(I) all: 0.346 / % possible all: 96.24

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Processing

Software
NameVersionClassification
PROTEUM2data collection
PROTEUM2data reduction
pointlessdata scaling
Aimlessdata scaling
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NBH

2nbh


Resolution: 2→43.8 Å / SU ML: 0.1117 / Cross valid method: FREE R-VALUE / Phase error: 27.5604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 316 5.01 %
Rwork0.2043 5993 -
obs-6317 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.06 Å2
Refinement stepCycle: LAST / Resolution: 2→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms594 0 9 50 653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035612
X-RAY DIFFRACTIONf_angle_d0.6281829
X-RAY DIFFRACTIONf_chiral_restr0.0412104
X-RAY DIFFRACTIONf_plane_restr0.003105
X-RAY DIFFRACTIONf_dihedral_angle_d6.068188
LS refinement shellResolution: 2→2.072 Å
RfactorNum. reflection% reflection
Rfree0.5689 29 4.93 %
Rwork0.4116 588 -
obs--96.24 %

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