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- PDB-4fbr: Crystal structure of the Myxococcus Xanthus hemagglutinin (MBHA) -

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Basic information

Entry
Database: PDB / ID: 4fbr
TitleCrystal structure of the Myxococcus Xanthus hemagglutinin (MBHA)
ComponentsMyxobacterial hemagglutinin
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 / Myxobacterial hemagglutinin
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.6 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: Myxobacterial hemagglutinin


Theoretical massNumber of molelcules
Total (without water)27,9371
Polymers27,9371
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.099, 76.099, 37.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Myxobacterial hemagglutinin / Lectin


Mass: 27936.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: mbhA / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P07386
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium sulphate, 0.1 M sodium cacodylate trihydrate (pH 6.5) and 30% polyethylene glycol 8000, 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 SATURN 944 / Detector: CCD / Date: Jun 11, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→32.95 Å / Num. all: 32197 / Num. obs: 31241 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.2 / Redundancy: 6.48 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2993 / % possible all: 88.8

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Processing

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

3s5v


Resolution: 1.6→32.95 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.904 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(I): 2.2 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21172 3126 10 %RANDOM
Rwork0.17794 ---
all0.18137 28963 --
obs0.18137 28106 97.04 %-
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: 29.851 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.21 Å2-0 Å2
2---0.43 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 0 243 2206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212045
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.922797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.85125.17287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.033158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211613
X-RAY DIFFRACTIONr_mcbond_it0.761.51312
X-RAY DIFFRACTIONr_mcangle_it1.24422091
X-RAY DIFFRACTIONr_scbond_it1.5613733
X-RAY DIFFRACTIONr_scangle_it2.2494.5699
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 210 -
Rwork0.24 1857 -
obs-2067 87.47 %

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