[English] 日本語
Yorodumi
- PDB-1loc: INTERACTION OF A LEGUME LECTIN WITH TWO COMPONENTS OF THE BACTERI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
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


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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
Components

-
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

-
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

-
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


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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more