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- PDB-4fbo: Crystal structure of the Pseudomonas fluorescens agglutinin (PFA) -

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Basic information

Entry
Database: PDB / ID: 4fbo
TitleCrystal structure of the Pseudomonas fluorescens agglutinin (PFA)
ComponentsPseudomonas fluorescens agglutinin
KeywordsCarbohydrate binding protein / beta-barrel / HIV-inactivating
Function / homologyLipocalin - #450 / OAA-family lectin sugar binding domain / OAA-family lectin sugar binding domain / Lipocalin / carbohydrate binding / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKoharudin, L.M.I. / Gronenborn, A.M.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural Insights into the Anti-HIV Activity of the Oscillatoria agardhii Agglutinin Homolog Lectin Family.
Authors: Koharudin, L.M. / Kollipara, S. / Aiken, C. / Gronenborn, A.M.
#1: Journal: Structure / Year: 2011
Title: Structural basis of the anti-HIV activity of the cyanobacterial Oscillatoria Agardhii agglutinin.
Authors: Koharudin, L.M. / Gronenborn, A.M.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Sep 13, 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

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Assembly

Deposited unit
A: Pseudomonas fluorescens agglutinin
B: Pseudomonas fluorescens agglutinin


Theoretical massNumber of molelcules
Total (without water)28,0482
Polymers28,0482
Non-polymers00
Water5,621312
1
A: Pseudomonas fluorescens agglutinin


Theoretical massNumber of molelcules
Total (without water)14,0241
Polymers14,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pseudomonas fluorescens agglutinin


Theoretical massNumber of molelcules
Total (without water)14,0241
Polymers14,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.982, 70.343, 62.307
Angle α, β, γ (deg.)90.00, 111.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-218-

HOH

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Components

#1: Protein Pseudomonas fluorescens agglutinin


Mass: 14024.218 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: Pfl01_0508 / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q3KJ04
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 42.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0 M sodium citrate and 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 8, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→28.14 Å / Num. all: 26011 / Num. obs: 24397 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2334 / % possible all: 90.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0044refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S5V

3s5v


Resolution: 1.7→28.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.452 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(I): 2.1 / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21523 2531 10.1 %RANDOM
Rwork0.17624 ---
all0.18015 23411 --
obs0.18015 22452 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.737 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-0 Å2-0.73 Å2
2---0.94 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 0 312 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212023
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.8982751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8925.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16115285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.178158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211638
X-RAY DIFFRACTIONr_mcbond_it0.6281.51285
X-RAY DIFFRACTIONr_mcangle_it1.06722029
X-RAY DIFFRACTIONr_scbond_it1.5833738
X-RAY DIFFRACTIONr_scangle_it2.2814.5721
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 167 -
Rwork0.276 1611 -
obs-1778 92.41 %

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