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Database: PDB / ID: 1loc
TitleINTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERIAL CELL WALL
Components
  • (LEGUME ISOLECTIN I ...) x 2
  • MURAMYL-DIPEPTIDE D-ALA-D-IGLN
KeywordsSUGAR BINDING PROTEIN / LECTIN
Function / homology
Function and homology information


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, 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
N-carboxyl-N-methyl-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)
synthetic construct (others)
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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 12, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_biol / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.oligomeric_count ..._pdbx_database_status.process_site / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Feb 21, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id

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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)
1: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
C: LEGUME ISOLECTIN I (ALPHA CHAIN)
D: LEGUME ISOLECTIN I (BETA CHAIN)
2: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
E: LEGUME ISOLECTIN I (ALPHA CHAIN)
F: LEGUME ISOLECTIN I (BETA CHAIN)
3: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
G: LEGUME ISOLECTIN I (ALPHA CHAIN)
H: LEGUME ISOLECTIN I (BETA CHAIN)
4: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,01124
Polymers103,39412
Non-polymers1,61712
Water5,729318
1
A: LEGUME ISOLECTIN I (ALPHA CHAIN)
B: LEGUME ISOLECTIN I (BETA CHAIN)
1: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
C: LEGUME ISOLECTIN I (ALPHA CHAIN)
D: LEGUME ISOLECTIN I (BETA CHAIN)
2: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,50512
Polymers51,6976
Non-polymers8096
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: LEGUME ISOLECTIN I (ALPHA CHAIN)
F: LEGUME ISOLECTIN I (BETA CHAIN)
3: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
G: LEGUME ISOLECTIN I (ALPHA CHAIN)
H: LEGUME ISOLECTIN I (BETA CHAIN)
4: MURAMYL-DIPEPTIDE D-ALA-D-IGLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,50512
Polymers51,6976
Non-polymers8096
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.580, 139.800, 63.400
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ALA A 80 - ASP A 81 OMEGA = 347.11 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 80 - ASP C 81 OMEGA = 347.61 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ALA E 80 - ASP E 81 OMEGA = 342.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ALA G 80 - ASP G 81 OMEGA = 346.01 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, ONE CA++ AND ONE MN++ ION, AND THE MURAMYL-DIPEPTIDE. THE ALPHA CHAIN CONSISTS OF 181 RESIDUES AND THE BETA CHAIN CONSISTS OF 52 RESIDUES. MONOMER 1 CONTAINS ALPHA CHAIN *A*, BETA CHAIN *B*, MURAMYL-DIPEPTIDE *1*, CA 228, AND MN 229. MONOMER 2 CONTAINS ALPHA CHAIN *C*, BETA CHAIN *D* AND MURAMYL- DIPEPTIDE *2*. MONOMERS 3 AND 4 ARE LABELLED SIMILARLY, WITH CHAIN IDENTIFIERS *E*, *F*, *3*, *G*, *H* AND *4*. EACH DIMER HAS 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 natural source / Source: (natural) Lathyrus ochrus (yellow-flowered pea) / Organ: SEED / References: UniProt: P04122
#2: Protein
LEGUME ISOLECTIN I (BETA CHAIN) / Lol I


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

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Protein/peptide / Sugars , 2 types, 8 molecules 1234

#3: Protein/peptide
MURAMYL-DIPEPTIDE D-ALA-D-IGLN


Mass: 217.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Sugar
ChemComp-MDP / N-carboxyl-N-methyl-beta-muramic acid / N-CARBOXY-N-METHYL-MURAMIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9

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Non-polymers , 3 types, 326 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE MURAMYL-DIPEPTIDE D-ALA-D-IGLN OCCURS 4 TIMES, ONCE IN EACH MONOMER. IT IS REPRESENTED AS MDP- ...THE MURAMYL-DIPEPTIDE D-ALA-D-IGLN OCCURS 4 TIMES, ONCE IN EACH MONOMER. IT IS REPRESENTED AS MDP-ALA-GLU-NH2. MDP IS N-CARBOXY-N-METHYL-MURAMIC ACID. THE LABELS ARE: MDP 1 950, ALA 1 951, GLU 1 952 AND NH2 1 953 MDP 2 960, ALA 2 961 (GLU AND NH2 NOT SEEN HERE) MDP 3 970, ALA 3 971, GLU 3 972 AND NH2 3 973 MDP 4 980, ALA 4 981, GLU 4 982 AND NH2 4 983
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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Details: reservoirs contain the same ingredients as drops, but twice as consentrated. taken from Bourne, Y. et al. (1988). J. Mol. Biol., 202, 685-687.
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: 57554 / % possible obs: 97 % / Num. measured all: 248619 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.05→6 Å / Rfactor Rwork: 0.189 / Rfactor obs: 0.189 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2.05→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7232 0 8 318 7558
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_deg3.2
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: 57175 / Rfactor obs: 0.189 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.2
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_deg1.3

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