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- PDB-2g3p: STRUCTURE OF THE N-TERMINAL TWO DOMAINS OF THE INFECTIVITY PROTEI... -

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Basic information

Entry
Database: PDB / ID: 2g3p
TitleSTRUCTURE OF THE N-TERMINAL TWO DOMAINS OF THE INFECTIVITY PROTEIN G3P OF FILAMENTOUS PHAGE FD
ComponentsINFECTIVITY PROTEIN G3P
KeywordsVIRAL PROTEIN / INFECTION / FILAMENTOUS PHAGE / PILUS BINDING / BETA BARREL / CONFORMATIONAL CHANGE
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 / MIRAS / Resolution: 1.9 Å
AuthorsHolliger, P. / Williams, R.L.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the two N-terminal domains of g3p from filamentous phage fd at 1.9 A: evidence for conformational lability.
Authors: Holliger, P. / Riechmann, L. / Williams, R.L.
History
DepositionOct 27, 1998Processing site: BNL
Revision 1.0Jul 19, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INFECTIVITY PROTEIN G3P
B: INFECTIVITY PROTEIN G3P


Theoretical massNumber of molelcules
Total (without water)49,1512
Polymers49,1512
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-17 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.220, 78.250, 62.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.865487, -0.02829, -0.500131), (-0.043205, -0.990468, 0.130792), (-0.499064, 0.134807, 0.856015)
Vector: 58.732, 52.105, 12.066)

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Components

#1: Protein INFECTIVITY PROTEIN G3P


Mass: 24575.518 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 2-DOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage fd (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / Plasmid: PUC119 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / Variant (production host): LAC / References: UniProt: P03661
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 3.2 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
24.3 Msodium formate1reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.947
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 1998 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 1.6→13.8 Å / Num. obs: 81474 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 4.7
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.45 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 58927 / % possible obs: 99.8 % / Num. measured all: 343352 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→13 Å / SU B: 3.5 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1499 3.1 %RANDOM
Rwork0.26 ---
obs-47624 99.7 %-
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 1.9→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 303 3463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0522
X-RAY DIFFRACTIONp_mcangle_it1.7443
X-RAY DIFFRACTIONp_scbond_it1.1212
X-RAY DIFFRACTIONp_scangle_it1.8543
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.299 / Rfactor Rwork: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

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