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- PDB-1j4t: Structure of Artocarpin: a Lectin with Mannose Specificity (Form 2) -

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Basic information

Entry
Database: PDB / ID: 1j4t
TitleStructure of Artocarpin: a Lectin with Mannose Specificity (Form 2)
ComponentsArtocarpin
KeywordsPLANT PROTEIN / all Beta / Greek Key motif / Beta prism I fold
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
Mannose-specific lectin KM+
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsPratap, J.V. / Jeyaprakash, A.A. / Rani, P.G. / Sekar, K. / Surolia, A. / Vijayan, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of artocarpin, a Moraceae lectin with mannose specificity, and its complex with methyl-alpha-D-mannose: implications to the generation of carbohydrate specificity.
Authors: Pratap, J.V. / Jeyaprakash, A.A. / Rani, P.G. / Sekar, K. / Surolia, A. / Vijayan, M.
History
DepositionOct 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Artocarpin
B: Artocarpin
C: Artocarpin
D: Artocarpin
E: Artocarpin
F: Artocarpin
G: Artocarpin
H: Artocarpin


Theoretical massNumber of molelcules
Total (without water)128,9368
Polymers128,9368
Non-polymers00
Water15,745874
1
A: Artocarpin
B: Artocarpin
C: Artocarpin
D: Artocarpin


Theoretical massNumber of molelcules
Total (without water)64,4684
Polymers64,4684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-37 kcal/mol
Surface area23290 Å2
MethodPISA
2
E: Artocarpin
F: Artocarpin
G: Artocarpin
H: Artocarpin


Theoretical massNumber of molelcules
Total (without water)64,4684
Polymers64,4684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-39 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.69, 72.19, 92.63
Angle α, β, γ (deg.)90.0, 101.15, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Artocarpin


Mass: 16116.977 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: seeds / Source: (natural) Artocarpus integer (campedak) / References: UniProt: Q7M1T4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: PBS Buffer, 20% PEG 1450, 10Mg/ml protein, pH 7.4, vapor diffusion, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1droppH7.4
20.15 M1dropNaCl
340 %methoxy PEG3501drop
440 %methoxy PEG3501reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 42342 / Num. obs: 42342 / % possible obs: 96.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.379 / % possible all: 56
Reflection
*PLUS
Num. measured all: 133210 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 56 % / Rmerge(I) obs: 0.379

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 2.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
Rfree0.258 -
Rwork0.191 -
obs-36759
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9048 0 0 874 9922
Refine LS restraintsType: x_bond_d / Dev ideal: 0.01
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.191 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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