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- PDB-2gvm: Crystal structure of hydrophobin HFBI with detergent -

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Basic information

Entry
Database: PDB / ID: 2gvm
TitleCrystal structure of hydrophobin HFBI with detergent
ComponentsHydrophobin-1
KeywordsSURFACE ACTIVE PROTEIN / hydrophobin / amphiphile / surfactant / high solvent content
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMay 3, 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: Derived calculations / Version format compliance
Revision 1.3Aug 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL ASSEMBLY IS AN OCTAMER FORMED IN THE PRESENCE OF DETERGENT BY 8 HFBI-MOLECULES AND 20 LDAO-MOLECULES.

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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)32,59916
Polymers30,1744
Non-polymers2,42512
Water2,126118
1
A: Hydrophobin-1
B: Hydrophobin-1
C: Hydrophobin-1
D: Hydrophobin-1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)65,19932
Polymers60,3498
Non-polymers4,85024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
2
A: Hydrophobin-1
C: Hydrophobin-1
hetero molecules

A: Hydrophobin-1
C: Hydrophobin-1
hetero molecules

B: Hydrophobin-1
D: Hydrophobin-1
hetero molecules

B: Hydrophobin-1
D: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,19932
Polymers60,3498
Non-polymers4,85024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation6_455-x-1/2,-y+1/2,z+1/21
crystal symmetry operation7_444-x-1/2,y-1/2,-z-1/21
Buried area10020 Å2
ΔGint-155 kcal/mol
Surface area32230 Å2
MethodPISA
3
D: Hydrophobin-1

D: Hydrophobin-1

B: Hydrophobin-1
hetero molecules

B: Hydrophobin-1
hetero molecules

A: Hydrophobin-1
C: Hydrophobin-1
hetero molecules

A: Hydrophobin-1
C: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,19932
Polymers60,3498
Non-polymers4,85024
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation7_444-x-1/2,y-1/2,-z-1/21
crystal symmetry operation6_455-x-1/2,-y+1/2,z+1/21
crystal symmetry operation8_454x-1/2,-y+1/2,-z-11
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area9350 Å2
ΔGint-146 kcal/mol
Surface area32900 Å2
MethodPISA
4
A: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0684
Polymers7,5441
Non-polymers5243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
B: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9858
Polymers7,5441
Non-polymers1,4427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
C: Hydrophobin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0023
Polymers7,5441
Non-polymers4592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
D: Hydrophobin-1


Theoretical massNumber of molelcules
Total (without water)7,5441
Polymers7,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.900, 121.600, 121.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe quaternary structure of the protein comprises of the asymmetric unit and its neighbor -1-x,y,-1/2-z. Thus, the biological assembly is comprised of eight protein molecules (four in each asymmetric unit) and 20 detergent molecules (10 in each asymmetric unit), forming a sandwich-like structures with the detergent molecules in the middle.

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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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 5.61 Å3/Da / Density % sol: 78.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M zinc acetate, 0.1 HEPES (pH 7) LDAO-detergent as an additive, concentration in the drop 2 mM, pH 7.0, 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: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2006
RadiationMonochromator: Si 111, horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 28109 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.06 / Net I/σ(I): 20.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.52 / Num. unique all: 3297 / Rsym value: 0.419 / % possible all: 91.7

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FZ6

2fz6


Resolution: 2.3→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1406 4.6 %random
Rwork0.233 ---
all0.233 28109 --
obs0.233 28109 92.1 %-
Solvent computationBsol: 42.293 Å2
Displacement parametersBiso mean: 42.472 Å2
Baniso -1Baniso -2Baniso -3
1--1.611 Å20 Å20 Å2
2--0.582 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 162 118 2248
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.59
X-RAY DIFFRACTIONc_mcbond_it1.4931.5
X-RAY DIFFRACTIONc_scbond_it2.1282
X-RAY DIFFRACTIONc_mcangle_it2.5732
X-RAY DIFFRACTIONc_scangle_it3.2822.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:act.paramCNS_TOPPAR:act.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:lda.paramCNS_TOPPAR:lda.top

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