[English] 日本語
Yorodumi
- PDB-2bv4: 1.0A Structure of Chromobacterium Violaceum Lectin in Complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bv4
Title1.0A Structure of Chromobacterium Violaceum Lectin in Complex with alpha-methyl-mannoside
ComponentsLECTIN CV-IIL
KeywordsLECTIN / MANNOSE / CHROMOBACTERIUM VIOLACEUM
Function / homology
Function and homology information


Calcium-mediated lectin / Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Calcium-mediated lectin domain-containing protein
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsPokorna, M. / Cioci, G. / Perret, S. / Rebuffet, E. / Adam, J. / Gilboa-Garber, N. / Mitchell, E.P. / Imberty, A. / Wimmerova, M.
CitationJournal: Biochemistry / Year: 2006
Title: Unusual Entropy Driven Affinity of Chromobacterium Violaceum Lectin Cv-Iil Towards Fucose and Mannose
Authors: Pokorna, M. / Cioci, G. / Perret, S. / Rebuffet, E. / Kostlanova, N. / Adam, J. / Gilboa-Garber, N. / Mitchell, E.P. / Imberty, A. / Wimmerova, M.
History
DepositionJun 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMIMATION METHOD: PROVIDED BY DEPOSITOR

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LECTIN CV-IIL
B: LECTIN CV-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2458
Polymers23,6962
Non-polymers5496
Water6,846380
1
A: LECTIN CV-IIL
B: LECTIN CV-IIL
hetero molecules

A: LECTIN CV-IIL
B: LECTIN CV-IIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49016
Polymers47,3924
Non-polymers1,09712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.685, 89.504, 46.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein LECTIN CV-IIL


Mass: 11848.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Plasmid: PET25(B) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER(DE3) / References: UniProt: Q7NX84
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Description: MOLREP WAS USED WITH MODEL 1GZT TO FIND THE POSITION OF 4 CA ATOMS IN THE A.U. PHASING WAS PERFORMED BY ACORN STARTING FROM THE POSITION OF THESE CA ATOMS
Crystal growDetails: PEG 8000 10%, 0.1M NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2004 / Details: MIRRORS
RadiationMonochromator: DIAMOND AND GE DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1→23.24 Å / Num. obs: 114226 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.02 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.48
Reflection shellResolution: 1→1.03 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.67 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZT

1gzt


Resolution: 1→46.47 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.464 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.123 5724 5 %RANDOM
Rwork0.107 ---
obs0.107 108432 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.43 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 30 380 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221942
X-RAY DIFFRACTIONr_bond_other_d0.0010.021775
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9642685
X-RAY DIFFRACTIONr_angle_other_deg2.09434145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.91225.94979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51415313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.651159
X-RAY DIFFRACTIONr_chiral_restr0.3510.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_nbd_refined0.2610.2338
X-RAY DIFFRACTIONr_nbd_other0.2070.21758
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21000
X-RAY DIFFRACTIONr_nbtor_other0.1020.21184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.216
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5571.51295
X-RAY DIFFRACTIONr_mcbond_other0.6211.5526
X-RAY DIFFRACTIONr_mcangle_it2.10722085
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7733705
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8964.5600
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 400 -
Rwork0.26 7463 -
obs--93.64 %

+
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