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- PDB-2fz6: Crystal structure of hydrophobin HFBI -

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Basic information

Entry
Database: PDB / ID: 2fz6
TitleCrystal structure of hydrophobin HFBI
ComponentsHydrophobin-1
KeywordsSURFACE ACTIVE PROTEIN / hydrophobin / beta barrel / pseudo-merohedral twinning / amphiphile
Function / homologyCerato-ulmin hydrophobin family / Fungal hydrophobin / hfbii hydrophobin / Hydrophobin / Hydrophobin superfamily / Alpha-Beta Barrel / extracellular region / Alpha Beta / Hydrophobin-1
Function and homology information
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsHakanpaa, J.M. / Rouvinen, J.
CitationJournal: Protein Sci. / Year: 2006
Title: Two crystal structures of Trichoderma reesei hydrophobin HFBI--The structure of a protein amphiphile with and without detergent interaction.
Authors: Hakanpaa, J.M. / Szilvay, G.R. / Kaljunen, H. / Maksimainen, M. / Linder, M. / Rouvinen, J.
History
DepositionFeb 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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-1
B: Hydrophobin-1
C: Hydrophobin-1
D: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4368
Polymers30,1744
Non-polymers2624
Water1,946108
1
A: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6743
Polymers7,5441
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6092
Polymers7,5441
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6092
Polymers7,5441
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hydrophobin-1


Theoretical massNumber of molelcules
Total (without water)7,5441
Polymers7,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: Hydrophobin-1
B: Hydrophobin-1
hetero molecules

A: Hydrophobin-1
B: Hydrophobin-1
hetero molecules

C: Hydrophobin-1
D: Hydrophobin-1
hetero molecules

C: Hydrophobin-1
D: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,87216
Polymers60,3498
Non-polymers5238
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area6320 Å2
ΔGint-244 kcal/mol
Surface area27040 Å2
MethodPISA
6
A: Hydrophobin-1
B: Hydrophobin-1
hetero molecules

C: Hydrophobin-1
D: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4368
Polymers30,1744
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area2420 Å2
ΔGint-137 kcal/mol
Surface area14360 Å2
MethodPISA
7
A: Hydrophobin-1
B: Hydrophobin-1
hetero molecules

C: Hydrophobin-1
D: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4368
Polymers30,1744
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area2130 Å2
ΔGint-115 kcal/mol
Surface area14550 Å2
MethodPISA
8


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-109 kcal/mol
Surface area13970 Å2
MethodPISA
9
A: Hydrophobin-1
B: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2835
Polymers15,0872
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-61 kcal/mol
Surface area7470 Å2
MethodPISA
10
C: Hydrophobin-1
D: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1533
Polymers15,0872
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-35 kcal/mol
Surface area7600 Å2
MethodPISA
11
B: Hydrophobin-1
hetero molecules

B: Hydrophobin-1
hetero molecules

D: Hydrophobin-1

D: Hydrophobin-1


Theoretical massNumber of molelcules
Total (without water)30,3056
Polymers30,1744
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area3240 Å2
ΔGint-91 kcal/mol
Surface area13670 Å2
MethodPISA
12
A: Hydrophobin-1
hetero molecules

C: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2835
Polymers15,0872
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area970 Å2
ΔGint-79 kcal/mol
Surface area7360 Å2
MethodPISA
13
A: Hydrophobin-1
hetero molecules

A: Hydrophobin-1
hetero molecules

C: Hydrophobin-1
hetero molecules

C: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,56710
Polymers30,1744
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area3420 Å2
ΔGint-170 kcal/mol
Surface area13240 Å2
MethodPISA
14
B: Hydrophobin-1
hetero molecules

D: Hydrophobin-1


Theoretical massNumber of molelcules
Total (without water)15,1533
Polymers15,0872
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_666-x+1,y+1,-z+11
Buried area590 Å2
ΔGint-38 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.900, 49.600, 85.800
Angle α, β, γ (deg.)90.00, 129.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer formed by the molecules in the asymmetric unit

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Components

#1: Protein
Hydrophobin-1 / / Hydrophobin I / HFBI


Mass: 7543.619 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / References: UniProt: P52754
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.98 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M zinc sulphate, 0.1M sodium cacodylate pH6.5, 9mM OSG, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 / Wavelength: 0.843 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 2004 / Details: Bent mirror
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. obs: 20790 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.8
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 6.42 / Num. unique all: 4909 / % possible all: 98.7

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1R2M

1r2m


Resolution: 2.1→10 Å / Num. parameters: 8340 / Num. restraintsaints: 8322 / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Pseudo-merohedral twinning. The twin law is -h, -k, h+l. The twin operator used in the Shelxl-refinement was TWIN -1 0 0 0 -1 0 1 0 1. The BASF-value refined to 0.49, so the twin fraction is 0.49.
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 1040 5.3 %RANDOM
all0.2238 19747 --
obs0.2239 19747 94.7 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2084
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 4 108 2084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0273
X-RAY DIFFRACTIONs_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.119
X-RAY DIFFRACTIONs_approx_iso_adps0

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