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- PDB-3knq: Beta Turn Optimization of the Gene-3-Protein of Filamentous Phage Fd -

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Basic information

Entry
Database: PDB / ID: 3knq
TitleBeta Turn Optimization of the Gene-3-Protein of Filamentous Phage Fd
ComponentsAttachment protein G3P
KeywordsVIRAL PROTEIN / filamentous phage / beta turn / rational design / protein stabilization / protein engineering / protein folding / Disulfide bond / Phage recognition / Transmembrane
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 speciesEnterobacteria phage fd (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsJakob, R.P. / Dobbek, H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Elimination of a cis-proline-containing loop and turn optimization stabilizes a protein and accelerates its folding.
Authors: Jakob, R.P. / Zierer, B.K. / Weininger, U. / Hofmann, S.D. / Lorenz, S.H. / Balbach, J. / Dobbek, H. / Schmid, F.X.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 13, 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999AUTHOR STATES THAT RESIDUES 157-162(GLN GLY THR ASP PRO VAL) OF UNP ENTRY P03661 WAS DELETED AND ...AUTHOR STATES THAT RESIDUES 157-162(GLN GLY THR ASP PRO VAL) OF UNP ENTRY P03661 WAS DELETED AND REPLACED BY RESIDUES 157-159 (VAL ASN GLY) IN THE CRYSTALLIZED PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Attachment protein G3P
B: Attachment protein G3P


Theoretical massNumber of molelcules
Total (without water)48,6352
Polymers48,6352
Non-polymers00
Water4,396244
1
A: Attachment protein G3P


Theoretical massNumber of molelcules
Total (without water)24,3181
Polymers24,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Attachment protein G3P


Theoretical massNumber of molelcules
Total (without water)24,3181
Polymers24,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.513, 86.974, 96.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Attachment protein G3P / Gene 3 protein / G3P / Minor coat protein


Mass: 24317.510 Da / Num. of mol.: 2 / Fragment: Gene-3-Protein, residue 19-238
Mutation: C7S, P11S, T13I, N15G, R29W, C36I, N39K, C46I, C53V, G55A, T56I, I60V, T101I, Q129H, N138G, R144V, Q145N, A147V, C188V, F199L, C201A, S207L, D209Y, Replacment of LoopQ157-V162 with the sequence VNG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage fd (virus) / Gene: 3, III / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P03661
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15-20% PEG3350, 0.2M NH4Cl, 0.05 M CaCl2, 0.1 M Tris/Cl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.13→33.77 Å / Num. obs: 26294 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 13.4 / Biso Wilson estimate: 35.88 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.13→2.19 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 47 / Num. unique all: 1532 / Rsym value: 0.02 / % possible all: 76.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dgs.PDB

3dgs


Resolution: 2.13→33.77 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 1323 5.03 %RANDOM
Rwork0.2139 ---
obs-26294 96.4 %-
Displacement parametersBiso mean: 54.37 Å2
Baniso -1Baniso -2Baniso -3
1--5.637 Å20 Å20 Å2
2--12.9022 Å20 Å2
3----7.2652 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.13→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 244 3196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.11
LS refinement shellResolution: 2.13→2.19 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2999 128 5.16 %
Rwork0.2839 2352 -

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