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- PDB-1tx9: gpd prior to capsid assembly -

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Basic information

Entry
Database: PDB / ID: 1tx9
Titlegpd prior to capsid assembly
ComponentsScaffolding protein D
KeywordsSTRUCTURAL PROTEIN / scaffolding protein / phiX174 / assembly / conformational switching
Function / homology
Function and homology information


viral procapsid maturation / host cell cytoplasm
Similarity search - Function
Procapsid Of Bacteriophage Phix174, Chain 1 / Scaffold protein D / Scaffold protein D / Scaffold protein D superfamily / Bacteriophage scaffolding protein D / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
External scaffolding protein D / External scaffolding protein D
Similarity search - Component
Biological speciesEnterobacteria phage phiX174 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsMorais, M.C. / Fisher, M. / Kanamaru, K. / Fane, B.A. / Rossmann, M.G.
CitationJournal: Mol.Cell / Year: 2004
Title: Conformational switching by the scaffolding protein D directs the assembly of bacteriophage phiX174
Authors: Morais, M.C. / Fisher, M. / Kanamaru, S. / Przybyla, L. / Burgner, J. / Fane, B.A. / Rossmann, M.G.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scaffolding protein D
B: Scaffolding protein D


Theoretical massNumber of molelcules
Total (without water)33,6442
Polymers33,6442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-21 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.440, 106.440, 127.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Scaffolding protein D / GPD


Mass: 16822.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Gene: D / Plasmid: pSE420 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03637, UniProt: P69486*PLUS

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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 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG(MME) 5500, NH4SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→49.09 Å / Num. all: 11395 / Num. obs: 11395 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Limit h max: 32 / Limit h min: 0 / Limit k max: 22 / Limit k min: 0 / Limit l max: 38 / Limit l min: 0 / Observed criterion F max: 244129.35 / Observed criterion F min: 0.55
Reflection shellResolution: 3.31→3.43 Å / % possible all: 84.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CD3

1cd3


Resolution: 3.31→49.09 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1089 10.1 %random
Rwork0.271 ---
all0.271 11395 --
obs0.28 10742 94.3 %-
Solvent computationSolvent model: bulk solvent / Bsol: 23.6913 Å2 / ksol: 0.288625 e/Å3
Displacement parametersBiso max: 79.15 Å2 / Biso mean: 22.44 Å2 / Biso min: 3.92 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å20 Å2
2---3.14 Å20 Å2
3---6.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.6 Å
Luzzati d res high-3.31
Refinement stepCycle: LAST / Resolution: 3.31→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 0 0 2125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg20.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.85
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.31-3.460.381079.10.36710690.0371392117684.5
3.46-3.640.4071118.90.30611410.0391387125290.2
3.64-3.870.30415711.80.28111710.0241394132895.3
3.87-4.170.281259.40.22412060.0251394133195.5
4.17-4.590.2521309.40.21512520.0221426138296.8
4.59-5.250.26614710.80.22412160.0221412136396.5
5.25-6.620.3381319.30.30312820.0291456141397
6.62-49.090.32118112.10.29813160.0241543149797
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top

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