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- PDB-3dgs: Changing the determinants of protein stability from covalent to n... -

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Basic information

Entry
Database: PDB / ID: 3dgs
TitleChanging the determinants of protein stability from covalent to non-covalent interactions by in-vitro evolution: a structural and energetic analysis
ComponentsCoat protein A
KeywordsVIRAL PROTEIN / protein stabilization / dissulfide bonds / evolutionary protein design / phage gene-3-protein / phage display / Capsid protein / Phage recognition / Virion
Function / homology
Function and homology information


viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / host cell membrane / viral capsid / entry receptor-mediated virion attachment to host cell / membrane
Similarity search - Function
Minor Coat Protein; domain 2 / Minor Coat Protein; Domain 2 / Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Roll / Alpha-Beta Complex ...Minor Coat Protein; domain 2 / Minor Coat Protein; Domain 2 / Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Attachment protein G3P
Similarity search - Component
Biological speciesBacteriophage fd (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJakob, R.P. / Kather, I. / Dobbek, H. / Schmid, F.X.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Changing the determinants of protein stability from covalent to non-covalent interactions by in vitro evolution: a structural and energetic analysis.
Authors: Kather, I. / Jakob, R.P. / Dobbek, H. / Schmid, F.X.
History
DepositionJun 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 16, 2012Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein A
B: Coat protein A


Theoretical massNumber of molelcules
Total (without water)49,5522
Polymers49,5522
Non-polymers00
Water4,648258
1
A: Coat protein A


Theoretical massNumber of molelcules
Total (without water)24,7761
Polymers24,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coat protein A


Theoretical massNumber of molelcules
Total (without water)24,7761
Polymers24,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.86, 92.21, 94.35
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coat protein A / G3P


Mass: 24775.959 Da / Num. of mol.: 2 / Fragment: residues 0-226
Mutation: C7S, P11S, T13I, N15G, R29W, C36I, N39K, C46I, C53V, G55A, T56I, I60V, T101I, Q129H, N138G, C188V, F199L, C201A, S207L, D209Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage fd (virus) / Gene: III / Production host: Escherichia coli (E. coli) / References: UniProt: P03661
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25-30% PEG 3350, 0.005M CaCl2, 0.2M NH4Cl, 0.1 Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 40287 / % possible obs: 99.5 % / Observed criterion σ(F): 1.9 / Redundancy: 2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / % possible all: 96.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G3P

2g3p


Resolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.263 5
Rwork0.216 -
obs-40287
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 0 0 258 3211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0086
X-RAY DIFFRACTIONc_angle_deg1.5

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