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- PDB-5exg: Crystal structure of recombinant dimeric Banana lectin -

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Basic information

Entry
Database: PDB / ID: 5exg
TitleCrystal structure of recombinant dimeric Banana lectin
ComponentsRipening-associated protein
KeywordsSUGAR BINDING PROTEIN / beta-prism I fold / lectin
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Ripening-associated protein
Similarity search - Component
Biological speciesMusa acuminata (dwarf banana)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsStruwe, W.B. / Allison, T.A. / Robinson, C.V. / Benesch, J.L.P.B.
Funding support United Kingdom, United States, 6items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)98101 United Kingdom
European Research Council26851 United Kingdom
Biotechnology and Biological Sciences Research Council United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM094919 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103390 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1UM1AI100663 United States
CitationJournal: To Be Published
Title: Glycan cluster recognition by a potent anti-HIV lectin exploiting bidentate binding amplified by tetrameric architecture
Authors: Hopper, J.T.S. / Grant, O.C. / Ambrose, S. / Krumm, S. / Allison, T.A. / Pritchard, L.K. / Tully, M. / Ozorowsky, G. / Ward, A.B. / Crispin, M. / Doores, K.J. / Woods, R.J. / Benesch, J.L.P. ...Authors: Hopper, J.T.S. / Grant, O.C. / Ambrose, S. / Krumm, S. / Allison, T.A. / Pritchard, L.K. / Tully, M. / Ozorowsky, G. / Ward, A.B. / Crispin, M. / Doores, K.J. / Woods, R.J. / Benesch, J.L.P.B. / Robinson, C.V. / Struwe, W.B.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 21, 2021Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ripening-associated protein
B: Ripening-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,99211
Polymers31,1752
Non-polymers8179
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-13 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.530, 63.330, 95.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Ripening-associated protein / Banlec


Mass: 15587.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musa acuminata (dwarf banana) / Strain: Cavendish / Plasmid: pBAN 3-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O22321
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: A protein solution [10 mg/mL, in 100 mM NaCl, 20mM Tris (pH 7.4)] was mixed 1:1 (v/v) with a reservoir solution containing 0.05 M NaBr, 0.1 M Bis Tris and 19% PEG 3350 (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 32288 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 25.046 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.137 / Χ2: 0.9 / Net I/σ(I): 15.77 / Num. measured all: 404818
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.740.7591.2322.0728995236622841.28396.5
1.74-1.790.8081.1012.429079231022811.14698.7
1.79-1.840.890.8543.1728612226922450.88998.9
1.84-1.90.9270.6454.2327269218521700.67299.3
1.9-1.960.9570.5215.4125407211720980.54499.1
1.96-2.030.9580.396.5822533206520180.40997.7
2.03-2.110.9850.3218.6325606199919840.33499.2
2.11-2.190.9870.2411.4124987192119100.2599.4
2.19-2.290.9890.2312.7323424184218290.2499.3
2.29-2.40.9910.20513.3623066176917660.21399.8
2.4-2.530.9930.17815.5322032169216870.18599.7
2.53-2.690.9940.14718.3319872158315790.15399.7
2.69-2.870.9960.11521.3617000151414820.1297.9
2.87-3.10.9980.09528.4517776140913940.09998.9
3.1-3.40.9990.07335.717327130913080.07699.9
3.4-3.80.9980.05744.3415144118311820.05999.9
3.8-4.390.9990.04946.5513050106510640.05199.9
4.39-5.380.9990.04449.01102279119080.04699.7
5.38-7.60.9990.04945.2884717216880.05195.4
7.60.9990.03651.8949414464110.03892.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.97 Å19.32 Å
Translation3.97 Å19.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BMY

2bmy


Resolution: 1.7→19.32 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.1522 / FOM work R set: 0.8596 / SU B: 2.037 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0951 / SU Rfree: 0.0941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1614 5 %RANDOM
Rwork0.1675 ---
obs0.1691 30642 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.09 Å2 / Biso mean: 19.988 Å2 / Biso min: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å20 Å2
2---0.89 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 1.7→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 49 164 2269
Biso mean--24.03 29.68 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192179
X-RAY DIFFRACTIONr_bond_other_d0.0020.022034
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.962931
X-RAY DIFFRACTIONr_angle_other_deg0.94134685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87923.17182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81715308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.166157
X-RAY DIFFRACTIONr_chiral_restr0.1240.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
X-RAY DIFFRACTIONr_mcbond_it1.8781.7411141
X-RAY DIFFRACTIONr_mcbond_other1.8751.7381140
X-RAY DIFFRACTIONr_mcangle_it2.8082.5931428
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 113 -
Rwork0.249 2150 -
all-2263 -
obs--96.5 %

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