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PDB | 2B7Y | Fava Bean Lectin-Glucose Complex

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Internal ID
31907
PDB Entry ID
2B7Y
Title
Fava Bean Lectin-Glucose Complex
Authors
Reeke Jr., G.N.,Becker, J.W.
Primary Citation
AuthorsReeke Jr., G.N., Becker, J.W.
TitleThree-dimensional structure of favin: saccharide binding-cyclic permutation in leguminous lectins
JournalScience, v.234, pp.1108 - 1111, 1986
AbstractView
Pubmed3775378
 
History
Deposition: 2005-10-05Release: 2005-10-18Last Modified: 2009-02-24
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
3.000.2270.2240.300P 21 21 21
Unit Cell
Length [Å]a90.00b89.30c67.40
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Favin beta chainresidues 1-182A, C
2Favin alpha chainresidues 183-233B, D
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Vicia fabafava beann/a
2Vicia fabafava beann/a
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
GLCALPHA-D-GLUCOSEC6H12O6[View][View]
NDG2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSEC8H15NO6[View][View]
MNMANGANESE (II) IONMn2[View][View]
CACALCIUM IONCa2[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordLECTIN
Textlectin-glucose complex, plant lectin, glycoprotein, carbohydrate binding protein, d-glucose, protein-carbohydrate complex, LECTIN
 
Polymeric Molecules
Chain A
DescriptionFavin beta chain
Fragmentresidues 1-182
Polymer typepolypeptide
Formula Weight19973.4
Source Methodnatural source
Entity Namelectin
Entity Name Sysn/a
 
Chain C
DescriptionFavin beta chain
Fragmentresidues 1-182
Polymer typepolypeptide
Formula Weight19973.4
Source Methodnatural source
Entity Namelectin
Entity Name Sysn/a
 
Chain B
DescriptionFavin alpha chain
Fragmentresidues 183-233
Polymer typepolypeptide
Formula Weight5573.3
Source Methodnatural source
Entity Namelectin
Entity Name Sysn/a
 
Chain D
DescriptionFavin alpha chain
Fragmentresidues 183-233
Polymer typepolypeptide
Formula Weight5573.3
Source Methodnatural source
Entity Namelectin
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,Cpolypeptide(L)n/a
2n/anonon/aB,Dpolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
GLCALPHA-D-GLUCOSEC6H12O6180.157View
NDG2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSEC8H15NO6221.210View
MNMANGANESE (II) IONMn254.938View
CACALCIUM IONCa240.080View
Natural/Genetically Modified Source
Common Namefava bean
Scientific NameVicia faba
Source GenusVicia
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Common Namefava bean
Scientific NameVicia faba
Source GenusVicia
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Crystallization Experiments
MethodMICRODIALYSIS
PH6.5
Temperature277.0
Details1 M glucose, 0.01 M sodium phosphate, pH 6.5, MICRODIALYSIS, temperature 277K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
90.0089.3067.40
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 21 21 21
Diffraction Detector
DetectorFILM
TypeFILM
Detailsn/a
Collection Daten/a
 
Diffraction Radiation
MonochromatorGraphite
Diffraction ProtocolSINGLE WAVELENGTH
Wavelength1.5418
Wavelength Listn/a
 
Diffraction Source
Sourcerotating-anode
TypeELLIOTT GX-6
Siten/a
Beamlinen/a
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)0.0
Resolution (High)3.00
Resolution (Low)46.18
Number Reflections (All) 10599
Number Reflections (Observed)10599
Percent Possible (Observed)93.0
R Merge I (Observed)n/a
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plot53.6
Redundancyn/a
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)3.00
Resolution (Low)46.18
Cut-off Sigma (F)0.0
Cut-off Sigma (I)n/a
Number of Reflections (All)10599
Number of Reflections (Observed)10599
Number of Reflections (R-Free) 545
Percent Reflections (Observed)92.71
R-Factor (All)0.227
R-Factor (Observed)0.227
R-Work0.224
R-Free0.3
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value25.733
Anisotropic B[1][1]1.40
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-2.20
Anisotropic B[2][3]0.00
Anisotropic B[3][3]0.80
 
Resolution Shells
Shell Resol (High)3.00
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)23
Number of Reflections (R-Work)578
R-Factor (R-Work)0.237
R-Factor (R-Free)0.424
R-Free Errorn/a
Percent Reflections (Observed)73.20
 
RMS Deviations
First|Previous|1 of 2|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.020
r_angle_refined_deg2.056
r_dihedral_angle_1_deg8.865
r_dihedral_angle_2_deg37.086
r_dihedral_angle_3_deg21.966
r_dihedral_angle_4_deg21.472
r_chiral_restr0.117
r_gen_planes_refined0.006
r_nbd_refined0.303
r_nbtor_refined0.347
First|Previous|1 of 2|Next|Last|
Coordinate Error
Luzzati ESD (Observed)0.35
Luzzati Sigma A (Observed)n/a
Luzzati Resolution Cutoff (Low)n/a
Luzzati ESD (R-Free Set)n/a
Luzzati Sigma A (R-Free Set)n/a
 
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms3556
Nucleic Acid Atoms0
Heterogen Atoms56
Solvent Atoms8
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)n/a
Data Reduction (data scaling)ROCKS
Structure SolutionCROWTHER
Structure RefinementREFMAC 5.2.0003
 
Software
Classificationrefinement
Software NameREFMAC5
 
Classificationdata extraction
Software Namepdb_extract
Software Version 1.700
 
Sequence Chain
A
Sequence
  1   TDEITSFSIP  KFRPDQPNLI  FQGGGYTTKE  KLTLTKAVKN  TVGRALYSLP  IHIWDSETGN

 61   VADFTTTFIF  VIDAPNGYNV  ADGFTFFIAP  VDTKPQTGGG  YLGVFNGKDY  DKTAQTVAVE

121   FDTFYNAAWD  PSNGKRHIGI  DVNTIKSIST  KSWNLQNGEE  AHVAISFNAT  TNVLSVTLLY

181   PN  

Sequence Chain
C
Sequence
  1   TDEITSFSIP  KFRPDQPNLI  FQGGGYTTKE  KLTLTKAVKN  TVGRALYSLP  IHIWDSETGN

 61   VADFTTTFIF  VIDAPNGYNV  ADGFTFFIAP  VDTKPQTGGG  YLGVFNGKDY  DKTAQTVAVE

121   FDTFYNAAWD  PSNGKRHIGI  DVNTIKSIST  KSWNLQNGEE  AHVAISFNAT  TNVLSVTLLY

181   PN  

Sequence Chain
B
Sequence
 1   LTGYTLSEVV  PLKDVVPEWV  RIGFSATTGA  EYATHEVLSW  TFLSELTGPS  N

Sequence Chain
D
Sequence
 1   LTGYTLSEVV  PLKDVVPEWV  RIGFSATTGA  EYATHEVLSW  TFLSELTGPS  N