[English] 日本語
Yorodumi
- PDB-1bjq: THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bjq
TitleTHE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE
ComponentsLECTIN
KeywordsGLYCOPROTEIN / LECTIN / ADENINE / QUATERNARY STRUCTURE / LEGUME LECTIN
Function / homology
Function and homology information


Legume lectin / 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 ...Legume lectin / 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
ADENINE / : / Seed lectin subunit I
Similarity search - Component
Biological speciesVigna unguiculata subsp. cylindrica (catjang)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.H. / Wyns, L. / Etzler, M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus.
Authors: Hamelryck, T.W. / Loris, R. / Bouckaert, J. / Dao-Thi, M.H. / Strecker, G. / Imberty, A. / Fernandez, E. / Wyns, L. / Etzler, M.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization of Two Related Lectins from the Legume Plant Dolichos Biflorus
Authors: Dao-Thi, M.-H. / Hamelryck, T.W. / Bouckaert, J. / Korber, F. / Burkow, V. / Poortmans, F. / Etzler, M. / Strecker, G. / Wyns, L. / Loris, R.
History
DepositionJun 26, 1998Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
E: LECTIN
F: LECTIN
G: LECTIN
H: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,76232
Polymers216,9218
Non-polymers1,84124
Water0
1
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,38116
Polymers108,4604
Non-polymers92112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: LECTIN
F: LECTIN
G: LECTIN
H: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,38116
Polymers108,4604
Non-polymers92112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.377, 116.135, 224.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.36395, -0.54215, -0.75737), (-0.35021, 0.67382, -0.65063), (0.86307, 0.50203, 0.05537)7.38717, 90.99081, -14.59116
2given(0.29801, -0.40533, 0.86423), (-0.57557, 0.64598, 0.50143), (-0.76152, -0.64686, -0.04079)-36.82518, 68.2079, 66.85284
3given(-0.37133, 0.53444, 0.75927), (0.52312, -0.55518, 0.64662), (0.76711, 0.6373, -0.07343)-27.85969, 47.91113, -10.21276
4given(-0.3112, -0.94379, 0.11141), (-0.94752, 0.2991, -0.11287), (0.0732, -0.14069, -0.98734)52.57348, 44.68594, 64.71711
5given(-1, -0.0066, -0.0057), (0.0053, -0.9805, 0.1965), (-0.0069, 0.1964, 0.9805)-20.3164, 140.4834, -14.0178
6given(-0.2983, 0.4087, -0.8626), (0.4004, -0.7668, -0.5017), (-0.8664, -0.495, 0.0651)15.877, 87.3511, 64.9051
7given(0.3142, 0.947, -0.0663), (0.9466, -0.3178, -0.0547), (-0.0729, -0.0455, -0.9963)-75.1321, 108.3493, 56.4041

-
Components

#1: Protein
LECTIN / / DBL


Mass: 27115.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: DOLICHOS BIFLORUS SEED LECTIN
Source: (gene. exp.) Vigna unguiculata subsp. cylindrica (catjang)
Species: Vigna unguiculata / Strain: subsp. cylindrica / Cell line: BL21 / Organ: SEEDSSeed / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P05045
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H5N5
Compound detailsTHE DOLICHOS BIFLORUS SEED LECTIN IS A HETEROTETRAMERIC LEGUME LECTIN COMPOSED OF TWO INTACT (253 ...THE DOLICHOS BIFLORUS SEED LECTIN IS A HETEROTETRAMERIC LEGUME LECTIN COMPOSED OF TWO INTACT (253 AA) AND TWO TRUNCATED SUBUNITS (244 AA). ONLY 235 RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY FOR THE TRUNCATED SUBUNITS (C, D, E AND F). THE ASYMMETRIC UNIT CONTAINS TWO TETRAMERS (CHAINS ABCD AND EFGH).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.5
Details: 100 MM NA-CACODYLATE PH 6.5 10 % (W/V) PEG 8000 20 MM MGAC2 1 MM ADENINE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Dao-Thi, M., (1998) Acta Crystallogr.,Sect.D, 54, 1446.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
38-12 %(w/v)PEG80001reservoir
420 mM1reservoirMgAc2
51
61
71

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 57851 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 6.5 / % possible all: 69.1
Reflection
*PLUS
Num. measured all: 162686
Reflection shell
*PLUS
Lowest resolution: 2.67 Å / Mean I/σ(I) obs: 2.5

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FAT

1fat


Resolution: 2.65→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5889 10.2 %RANDOM
Rwork0.219 ---
obs0.219 57851 92.5 %-
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14602 0 96 0 14698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.450.35
X-RAY DIFFRACTIONx_mcangle_it2.490.35
X-RAY DIFFRACTIONx_scbond_it1.450.4
X-RAY DIFFRACTIONx_scangle_it2.130.4
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTSX-RAY DIFFRACTION00
22X-RAY DIFFRACTION00
33X-RAY DIFFRACTION00
44X-RAY DIFFRACTION00
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.359 432 10 %
Rwork0.326 3888 -
obs--70.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.45
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor obs: 0.326

+
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