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- PDB-3p8s: Crystal structure of single chain recombinant jacalin showing hig... -

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Basic information

Entry
Database: PDB / ID: 3p8s
TitleCrystal structure of single chain recombinant jacalin showing highly dynamic posttranslational excission loop that reduces binding affinity
ComponentsJacalin
KeywordsSUGAR BINDING PROTEIN / Recombinant Jacalin / Hemeagglutinin / Sugars
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-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesArtocarpus heterophyllus (jackfruit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSharma, U. / Ahmed, N. / Krishnasastry, M.V. / Suresh, C.G.
CitationJournal: To Be Published
Title: Crystal Structure of Single Chain Recombinant Jacalin Showin Highly Dynamic Posttranslational Excission Loop that Reduce Binding Affinity
Authors: Sharma, U. / Ahmed, N. / Krishnasastry, M.V. / Suresh, C.G.
History
DepositionOct 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Jacalin
B: Jacalin


Theoretical massNumber of molelcules
Total (without water)33,9322
Polymers33,9322
Non-polymers00
Water1,892105
1
A: Jacalin
B: Jacalin

A: Jacalin
B: Jacalin


Theoretical massNumber of molelcules
Total (without water)67,8644
Polymers67,8644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area8400 Å2
ΔGint-35 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.878, 42.157, 73.586
Angle α, β, γ (deg.)90.00, 122.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Jacalin /


Mass: 16966.031 Da / Num. of mol.: 2 / Fragment: beta-chain, alpha-chain / Mutation: F112L,Y210C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artocarpus heterophyllus (jackfruit) / Gene: PSK3-JA3 / Plasmid: PT7NC / Production host: Escherichia coli (E. coli) / References: UniProt: Q38723
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate buffer, 15%(w/v) PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 26, 2007 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→62.6 Å / Num. obs: 19935 / % possible obs: 94.1 % / Redundancy: 1.13 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.13 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 11.6 / Num. unique all: 19935 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAC

1jac


Resolution: 2→56.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.409 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 1022 5.1 %RANDOM
Rwork0.17843 ---
obs0.18013 18885 93.97 %-
all-19935 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.286 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→56.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 0 105 2423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222376
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.9563225
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7924.52695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61615370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.004154
X-RAY DIFFRACTIONr_chiral_restr0.0820.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.51482
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13522393
X-RAY DIFFRACTIONr_scbond_it1.63894
X-RAY DIFFRACTIONr_scangle_it2.6324.5832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 51 -
Rwork0.198 1022 -
obs-18885 68.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80680.24720.05490.25870.14231.1395-0.01060.1866-0.07750.04910.0449-0.0365-0.06140.0143-0.03440.04150.00060.00780.0647-0.02790.032521.419220.393740.3136
21.25820.13850.08960.2629-0.17170.92440.06150.059-0.04010.02270.0358-0.0029-0.0479-0.1161-0.09730.03080.018-0.00260.02220.01430.0651-0.489718.439554.8326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 157
2X-RAY DIFFRACTION2B1 - 157

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