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- PDB-3ipv: Crystal structure of Spatholobus parviflorus seed lectin -

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Basic information

Entry
Database: PDB / ID: 3ipv
TitleCrystal structure of Spatholobus parviflorus seed lectin
Components
  • Lectin alpha chain
  • Lectin beta chain
KeywordsSUGAR BINDING PROTEIN / Galactose binding / Seed lectin / Hemagglutinin / Legume lectin / Anti fungal
Function / homology
Function and homology information


defense response to fungus / manganese ion binding / carbohydrate binding / killing of cells of another organism / calcium ion binding / protein-containing complex
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Seed lectin alpha chain / Seed lectin beta chain
Similarity search - Component
Biological speciesSpatholobus parviflorus (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsGeethanandan, K. / Bharath, S.R. / Abhilash, J. / Sadasivan, C. / Haridas, M.
CitationJournal: Int.J.Biol.Macromol. / Year: 2011
Title: X-ray structure of a galactose-specific lectin from Spatholobous parviflorous
Authors: Geethanandan, K. / Abhilash, J. / Bharath, S.R. / Sadasivan, C. / Haridas, M.
History
DepositionAug 18, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin alpha chain
B: Lectin beta chain
C: Lectin alpha chain
D: Lectin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,58012
Polymers103,2004
Non-polymers3808
Water12,484693
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-30 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.998, 60.792, 78.179
Angle α, β, γ (deg.)101.32, 91.38, 104.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lectin alpha chain


Mass: 26336.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spatholobus parviflorus (plant) / References: UniProt: P86352*PLUS
#2: Protein Lectin beta chain


Mass: 25263.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spatholobus parviflorus (plant) / References: UniProt: P86353*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITOR GUIDED BY THE SEQUENCE OF THE MODEL (OF MOLECULAR REPLACEMENT)POLYPEPTIDE. THE ...THE DEPOSITOR GUIDED BY THE SEQUENCE OF THE MODEL (OF MOLECULAR REPLACEMENT)POLYPEPTIDE. THE AMBIGUITY AT CERTAIN PLACES IN INTERPRETING ELECTRON DENSITY (E.G. ASP/ASN, ETC.) FOR SEQUENCE CAN NOT BE RULED OUT. A BREAK IS FOUND IN THE ELECTRON DENSITY MAP CALCULATED USING THE X-RAY DIFFRACTION DATA. IN THE CASE OF SPATHOLOBUS PARVIFLORUS ALPHA CHAIN, THE BREAK FOUND MAY ACCOMMODATE A MINIMUM OF TWO RESIDUES. HENCE, THE ABOVE SEQUENCE IS PROVIDED AS UNK (240, 241).

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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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 8000, 0.2M Phosphate Buffer Saline, 5% MPD, 5% Iso propanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 12, 2009 / Details: MIRROR
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→31 Å / Num. obs: 62376 / % possible obs: 90.5 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.1
Reflection shellResolution: 2.04→2.14 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 3.1 / Num. unique all: 59144 / % possible all: 73.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPAUTO MRphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LU1

1lu1


Resolution: 2.04→19.82 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.923 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.5 / σ(I): 2 / ESU R: 0.23 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26442 3179 5.1 %RANDOM
Rwork0.19857 ---
all0.1986 67450 --
obs0.20197 59144 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.812 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.04→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 8 693 7987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227469
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.94910218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33324.599274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.344151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9991512
X-RAY DIFFRACTIONr_chiral_restr0.1390.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215622
X-RAY DIFFRACTIONr_mcbond_it1.0011.54848
X-RAY DIFFRACTIONr_mcangle_it1.60727825
X-RAY DIFFRACTIONr_scbond_it2.90132621
X-RAY DIFFRACTIONr_scangle_it3.814.52393
LS refinement shellResolution: 2.042→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 205 -
Rwork0.246 3789 -
obs--80.23 %
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)
11.0243-0.37040.15920.7513-0.07411.6323-0.02640.07530.077-0.09160.0104-0.0942-0.08830.11920.0160.0236-0.01160.01240.01930.00980.0325-0.40220.2372-0.1846
20.8309-0.2741-0.23480.80780.07131.2444-0.04550.0688-0.0877-0.09990.0150.10550.0915-0.13170.03050.0354-0.0089-0.01580.027-0.01840.0604-17.517-27.1538-0.6128
30.9214-0.2892-0.06910.8540.07971.1320.0093-0.0872-0.1170.07-0.04170.05870.1457-0.03040.03240.0265-0.0080.01260.04330.01950.0626-19.9108-24.386536.0754
40.8907-0.24740.07020.8393-0.06351.26060.0103-0.07720.08870.0778-0.0323-0.0405-0.13750.06380.0220.0247-0.0102-0.0110.0522-0.00670.05742.7567-1.217736.6127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 251
2X-RAY DIFFRACTION2B1 - 239
3X-RAY DIFFRACTION3C1 - 251
4X-RAY DIFFRACTION4D1 - 239

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