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- PDB-1lod: INTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERI... -

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Basic information

Entry
Database: PDB / ID: 1lod
TitleINTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERIAL CELL WALL
Components(LEGUME ISOLECTIN I ...) x 2
KeywordsLECTIN
Function / homology
Function and homology information


D-mannose binding / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / beta-muramic acid / Lectin beta-1 and beta-2 chains / Mannose/glucose-specific lectin alpha 1 chain
Similarity search - Component
Biological speciesLathyrus ochrus (yellow-flowered pea)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsBourne, Y. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 1994
Title: Interaction of a legume lectin with two components of the bacterial cell wall. A crystallographic study.
Authors: Bourne, Y. / Ayouba, A. / Rouge, P. / Cambillau, C.
History
DepositionJan 27, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,91020
Polymers102,5258
Non-polymers1,38512
Water5,621312
1
A: LEGUME ISOLECTIN I (ALPHA CHAIN)
B: LEGUME ISOLECTIN I (BETA CHAIN)
C: LEGUME ISOLECTIN I (ALPHA CHAIN)
D: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,95510
Polymers51,2624
Non-polymers6936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: LEGUME ISOLECTIN I (ALPHA CHAIN)
F: LEGUME ISOLECTIN I (BETA CHAIN)
G: LEGUME ISOLECTIN I (ALPHA CHAIN)
H: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,95510
Polymers51,2624
Non-polymers6936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
G: LEGUME ISOLECTIN I (ALPHA CHAIN)
H: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9775
Polymers25,6312
Non-polymers3463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-54 kcal/mol
Surface area9380 Å2
MethodPISA
4
C: LEGUME ISOLECTIN I (ALPHA CHAIN)
D: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9775
Polymers25,6312
Non-polymers3463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-56 kcal/mol
Surface area9380 Å2
MethodPISA
5
A: LEGUME ISOLECTIN I (ALPHA CHAIN)
B: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9775
Polymers25,6312
Non-polymers3463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-57 kcal/mol
Surface area9690 Å2
MethodPISA
6
E: LEGUME ISOLECTIN I (ALPHA CHAIN)
F: LEGUME ISOLECTIN I (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9775
Polymers25,6312
Non-polymers3463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-56 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.400, 139.800, 62.700
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ALA A 80 - ASP A 81 OMEGA = 349.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 80 - ASP C 81 OMEGA = 347.69 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ALA E 80 - ASP E 81 OMEGA = 346.68 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ALA G 80 - ASP G 81 OMEGA = 343.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
DetailsTHIS CRYSTAL FORM CONTAINS TWO DIMERS IN THE ASYMMETRIC UNIT. EACH MONOMER CONSISTS OF TWO SEPARATE POLYPEPTIDE CHAINS, ALPHA AND BETA. THE ALPHA CHAIN CONSISTS OF 181 RESIDUES AND THE BETA CHAIN CONSISTS OF 52 RESIDUES. THE BETA AND ALPHA CHAINS OF MONOMER 1 HAVE BEEN ASSIGNED *A* AND *B*. THE BETA AND ALPHA CHAINS OF MONOMER 2 HAVE BEEN ASSIGNED *C* AND *D*. THE SAME ASSIGNMENT HAS BEEN MADE FOR THE SECOND MOLECULE WITH CHAIN IDENTIFIERS *E*, *F*, *G*, *H*. EACH DIMER HAS THE TWO MONOMERS WHICH ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS.

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Components

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LEGUME ISOLECTIN I ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
LEGUME ISOLECTIN I (ALPHA CHAIN)


Mass: 19847.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P04122
#2: Protein
LEGUME ISOLECTIN I (BETA CHAIN)


Mass: 5783.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P12306

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Sugars , 1 types, 4 molecules

#5: Sugar
ChemComp-MUR / beta-muramic acid / muramic acid


Type: D-saccharide, beta linking / Mass: 251.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO7
IdentifierTypeProgram
b-D-GlcpN3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 320 molecules

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: LEC1_LATOC SWISS-PROT RESIDUE PDB ATOM RECORDS NAME NUMBER NAME CHAIN SEQ/INSERT CODE LYS 153 ALA A 153 PHE 41 TYR B 41 LYS 153 ALA C 153 PHE 41 TYR D 41 LYS 153 ALA E 153 PHE 41 TYR F 41 LYS 153 ALA G 153 PHE 41 TYR H 41

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Details: Bourne, Y., (1990) Proteins Struct. Funct. Genet., 8, 365.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
240 %(v/v)MPD1drop
30.05 M1dropNaCl
40.02 MHEPES1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 6 Å / Num. obs: 56334 / % possible obs: 95 % / Num. measured all: 224984 / Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.05→6 Å / Rfactor Rwork: 0.197 / Rfactor obs: 0.197 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.05→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 76 312 7490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.3
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 55620 / Rfactor obs: 0.197 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.2
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_deg1.3

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