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- PDB-1lgc: INTERACTION OF A LEGUME LECTIN WITH THE N2 FRAGMENT OF HUMAN LACT... -

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Basic information

Entry
Database: PDB / ID: 1lgc
TitleINTERACTION OF A LEGUME LECTIN WITH THE N2 FRAGMENT OF HUMAN LACTOTRANSFERRIN OR WITH THE ISOLATED BIANTENNARY GLYCOPEPTIDE: ROLE OF THE FUCOSE MOIETY
Components
  • (LEGUME ISOLECTIN II ...) x 2
  • DIPEPTIDE
KeywordsLECTIN
Function / homology
Function and homology information


mannose binding / metal ion binding
Legume lectin, alpha chain, conserved site / Legume lectin domain / Concanavalin A-like lectin/glucanase domain superfamily / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Legume lectins beta-chain signature. / Legume lectins alpha-chain signature.
Lectin beta-1 and beta-2 chains / Mannose/glucose-specific lectin alpha 2 chain
Biological speciesLathyrus ochrus (yellow-flowered pea)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBourne, Y. / Cambillau, C.
CitationJournal: Structure / Year: 1994
Title: Structures of a legume lectin complexed with the human lactotransferrin N2 fragment, and with an isolated biantennary glycopeptide: role of the fucose moiety.
Authors: Bourne, Y. / Mazurier, J. / Legrand, D. / Rouge, P. / Montreuil, J. / Spik, G. / Cambillau, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 7, 1994 / Release: Aug 31, 1994
RevisionDateData content typeGroupProviderType
1.0Aug 31, 1994Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEGUME ISOLECTIN II (ALPHA CHAIN)
H: DIPEPTIDE
B: LEGUME ISOLECTIN II (BETA CHAIN)
C: LEGUME ISOLECTIN II (ALPHA CHAIN)
I: DIPEPTIDE
D: LEGUME ISOLECTIN II (BETA CHAIN)
E: LEGUME ISOLECTIN II (ALPHA CHAIN)
J: DIPEPTIDE
F: LEGUME ISOLECTIN II (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,21044
Polymers78,1589
Non-polymers6,05235
Water5,026279
1
A: LEGUME ISOLECTIN II (ALPHA CHAIN)
H: DIPEPTIDE
B: LEGUME ISOLECTIN II (BETA CHAIN)
C: LEGUME ISOLECTIN II (ALPHA CHAIN)
I: DIPEPTIDE
D: LEGUME ISOLECTIN II (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,08729
Polymers52,1056
Non-polymers3,98123
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: LEGUME ISOLECTIN II (ALPHA CHAIN)
J: DIPEPTIDE
F: LEGUME ISOLECTIN II (BETA CHAIN)
hetero molecules

E: LEGUME ISOLECTIN II (ALPHA CHAIN)
J: DIPEPTIDE
F: LEGUME ISOLECTIN II (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,24730
Polymers52,1056
Non-polymers4,14224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
γ
α
β
Length a, b, c (Å)117.000, 117.000, 120.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: ALA A 80 - ASP A 81 OMEGA = 359.01 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 80 - ASP C 81 OMEGA = 1.25 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ALA E 80 - ASP E 81 OMEGA = 0.80 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

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LEGUME ISOLECTIN II ... , 2 types, 6 molecules ACEBDF

#1: Protein/peptide LEGUME ISOLECTIN II (ALPHA CHAIN)


Mass: 19860.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lathyrus ochrus (yellow-flowered pea) / References: UniProt: P04122
#3: Protein/peptide LEGUME ISOLECTIN II (BETA CHAIN)


Mass: 5931.460 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
References: UniProt: P12307

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Protein/peptide , 1 types, 3 molecules HIJ

#2: Protein/peptide DIPEPTIDE /


Mass: 260.247 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

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Non-polymers , 10 types, 314 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Calcium
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Manganese
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#7: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#8: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#9: Chemical ChemComp-GAL / BETA-D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Galactose
#10: Chemical
ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
#11: Chemical ChemComp-SIA / O-SIALIC ACID


Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
#12: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O / Water

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Details

Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: LECB_LATOC SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 16 PRO A 16 ALA 168 GLY A 168 GLN 16 PRO C 16 ALA 168 GLY C 168 GLN 16 PRO E 16 ALA 168 GLY E 168

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS

Crystal-ID: 1 / Sol-ID: drop

IDConc.Common name
130-35 %(v/v)MPD
220 mg/mlprotein

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 24967 / % possible obs: 98 % / Num. measured all: 132152 / Rmerge(I) obs: 0.13

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6 Å / Rfactor Rwork: 0.185 / Rfactor obs: 0.185 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5399 0 366 279 6044
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 18097

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