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- PDB-7kmv: Structure of Malaysian Banana Lectin F84T -

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Basic information

Entry
Database: PDB / ID: 7kmv
TitleStructure of Malaysian Banana Lectin F84T
ComponentsJacalin-type lectin domain-containing protein
KeywordsSUGAR BINDING PROTEIN / MANNOSE-SPECIFIC JACALIN-RELATED LECTIN
Function / homologyJacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / carbohydrate binding / Jacalin-type lectin domain-containing protein
Function and homology information
Biological speciesMusa acuminata (dwarf banana)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-15-1-0067 United States
CitationJournal: Sci Rep / Year: 2021
Title: Targeted disruption of pi-pi stacking in Malaysian banana lectin reduces mitogenicity while preserving antiviral activity.
Authors: Coves-Datson, E.M. / King, S.R. / Legendre, M. / Swanson, M.D. / Gupta, A. / Claes, S. / Meagher, J.L. / Boonen, A. / Zhang, L. / Kalveram, B. / Raglow, Z. / Freiberg, A.N. / Prichard, M. / ...Authors: Coves-Datson, E.M. / King, S.R. / Legendre, M. / Swanson, M.D. / Gupta, A. / Claes, S. / Meagher, J.L. / Boonen, A. / Zhang, L. / Kalveram, B. / Raglow, Z. / Freiberg, A.N. / Prichard, M. / Stuckey, J.A. / Schols, D. / Markovitz, D.M.
History
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Jacalin-type lectin domain-containing protein
B: Jacalin-type lectin domain-containing protein
C: Jacalin-type lectin domain-containing protein
D: Jacalin-type lectin domain-containing protein
E: Jacalin-type lectin domain-containing protein
F: Jacalin-type lectin domain-containing protein
G: Jacalin-type lectin domain-containing protein
H: Jacalin-type lectin domain-containing protein
I: Jacalin-type lectin domain-containing protein
J: Jacalin-type lectin domain-containing protein
K: Jacalin-type lectin domain-containing protein
L: Jacalin-type lectin domain-containing protein
M: Jacalin-type lectin domain-containing protein
N: Jacalin-type lectin domain-containing protein
O: Jacalin-type lectin domain-containing protein
P: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,66736
Polymers259,74616
Non-polymers1,92120
Water35,8321989
1
A: Jacalin-type lectin domain-containing protein
B: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6604
Polymers32,4682
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-28 kcal/mol
Surface area11910 Å2
MethodPISA
2
C: Jacalin-type lectin domain-containing protein
D: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7565
Polymers32,4682
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-41 kcal/mol
Surface area12000 Å2
MethodPISA
3
E: Jacalin-type lectin domain-containing protein
F: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8536
Polymers32,4682
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-58 kcal/mol
Surface area12080 Å2
MethodPISA
4
G: Jacalin-type lectin domain-containing protein
H: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6604
Polymers32,4682
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-27 kcal/mol
Surface area12290 Å2
MethodPISA
5
I: Jacalin-type lectin domain-containing protein
J: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6604
Polymers32,4682
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-27 kcal/mol
Surface area12100 Å2
MethodPISA
6
K: Jacalin-type lectin domain-containing protein
L: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7565
Polymers32,4682
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-39 kcal/mol
Surface area11970 Å2
MethodPISA
7
M: Jacalin-type lectin domain-containing protein
N: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6604
Polymers32,4682
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-27 kcal/mol
Surface area12200 Å2
MethodPISA
8
O: Jacalin-type lectin domain-containing protein
P: Jacalin-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6604
Polymers32,4682
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-26 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.247, 157.871, 204.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Jacalin-type lectin domain-containing protein


Mass: 16234.124 Da / Num. of mol.: 16 / Mutation: F84T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musa acuminata (dwarf banana) / Production host: Escherichia coli (E. coli) / References: UniProt: M0TZ81
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1989 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.8M Ammonium Sulfate, 5% Peg 400, 0.1M MES 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 234462 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 21.07 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.09 / Χ2: 0.902 / Net I/σ(I): 6.7 / Num. measured all: 1657573
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.90.662115700.9180.2710.7160.65999.5
1.83-1.866.90.578115340.9270.2360.6250.68399.6
1.86-1.96.90.492116310.960.2010.5320.73999.7
1.9-1.946.90.461116360.940.1880.4980.93999.7
1.94-1.9870.342116020.9660.1390.370.76899.7
1.98-2.0370.272116660.9790.1110.2950.76799.8
2.03-2.0870.258116140.9790.1060.280.94299.9
2.08-2.1370.207116640.9890.0840.2240.84699.9
2.13-2.27.10.185116480.990.0750.20.85499.9
2.2-2.2770.215116590.9870.0880.2321.13899.9
2.27-2.357.10.163117310.9940.0660.1770.91299.9
2.35-2.447.10.141116590.9930.0570.1520.904100
2.44-2.557.10.118117480.9960.0480.1280.88599.9
2.55-2.697.20.101116850.9960.0410.1090.90499.9
2.69-2.867.30.085117450.9970.0340.0910.921100
2.86-3.087.30.075117880.9970.030.0811.056100
3.08-3.397.30.064118360.9980.0260.0691.19100
3.39-3.887.30.056118480.9980.0220.061.14299.9
3.88-4.887.10.047118920.9980.0190.0510.95899.3
4.88-5070.045123060.9980.0190.0490.7999.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BMY

2bmy


Resolution: 1.8→49.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.23 11266 4.9 %RANDOM
Rwork0.198 ---
obs0.199 229852 97.7 %-
Displacement parametersBiso max: 146.48 Å2 / Biso mean: 22.7 Å2 / Biso min: 6.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.2773 Å20 Å20 Å2
2---0.3116 Å20 Å2
3---0.0343 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.8→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16876 0 100 1989 18965
Biso mean--85.39 33.83 -
Num. residues----2245
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5654SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3007HARMONIC5
X-RAY DIFFRACTIONt_it17471HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2312SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact20808SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17471HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg23714HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion16.05
LS refinement shellResolution: 1.8→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2235 212 4.61 %
Rwork0.2045 4386 -
all0.2054 4598 -
obs--74.43 %

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