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- PDB-2chh: RALSTONIA SOLANACEARUM HIGH-AFFINITY MANNOSE-BINDING LECTIN -

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Basic information

Entry
Database: PDB / ID: 2chh
TitleRALSTONIA SOLANACEARUM HIGH-AFFINITY MANNOSE-BINDING LECTIN
ComponentsPROTEIN RSC3288
KeywordsLECTIN / SUGAR-BINDING PROTEIN / D-MANNOSE / PLANT PATHOGEN / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Probable sugar-binding lectin protein
Similarity search - Component
Biological speciesRALSTONIA SOLANACEARUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsMitchell, E.P. / Wimmerova, M. / Imberty, A.
CitationJournal: Mol. Microbiol. / Year: 2004
Title: A new Ralstonia solanacearum high-affinity mannose-binding lectin RS-IIL structurally resembling the Pseudomonas aeruginosa fucose-specific lectin PA-IIL.
Authors: Sudakevitz, D. / Kostlanova, N. / Blatman-Jan, G. / Mitchell, E.P. / Lerrer, B. / Wimmerova, M. / Katcoff, D.J. / Imberty, A. / Gilboa-Garber, N.
History
DepositionMar 15, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionMar 16, 2006ID: 1VYY
Revision 1.0Mar 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id
Revision 2.1Jul 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.name / _chem_comp.type ..._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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_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_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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 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 DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN RSC3288
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1796
Polymers11,7391
Non-polymers4405
Water3,963220
1
A: PROTEIN RSC3288
hetero molecules

A: PROTEIN RSC3288
hetero molecules

A: PROTEIN RSC3288
hetero molecules

A: PROTEIN RSC3288
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,71824
Polymers46,9564
Non-polymers1,76220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.292, 62.064, 74.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

21A-2181-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN RSC3288 / RALSTONIA SOLANACEARUM HIGH-AFFINITY MANNOSE-BINDING LECTIN RS2L


Mass: 11738.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RALSTONIA SOLANACEARUM (bacteria) / Plasmid: PET25B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XUA5

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Sugars , 2 types, 2 molecules

#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 223 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 48 %
Description: MOLECULAR REPLACEMENT WAS USED TO LOCATE THE CALCIUM POSITIONS AND THEN ACORN TO GENERATE PHASING FOR FULL MODEL RECONSTRUCTION WITH ARPWARP
Crystal growpH: 8.2
Details: 5UL DROPS OF 10MG/ML PROTEIN DISSOLVED IN WATER MIXED WITH 5UL DROPS OF 8% PEG 10000, 0.1M TRIS HCL, PH 8.2 WITH MANNOSE AT 270UG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1→18.6 Å / Num. obs: 73738 / % possible obs: 99 % / Redundancy: 2.92 % / Biso Wilson estimate: 5.58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.68
Reflection shellResolution: 1→1.01 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.65 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UQX

1uqx


Resolution: 1→18.47 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.371 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MET 90 IS MODELLED AS TWO CONFORMATIONS. UNK 1 IS AN UNKNOWN ATOM NEARBY TO MET 90. THE MET 90 CONFORMER B HAS AN UNUSUALLY SHORT SD-CE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MET 90 IS MODELLED AS TWO CONFORMATIONS. UNK 1 IS AN UNKNOWN ATOM NEARBY TO MET 90. THE MET 90 CONFORMER B HAS AN UNUSUALLY SHORT SD-CE BOND LENGTH. THIS COULD BE DUE TO RADIATION DAMAGE EFFECTS THAT WERE NOT UNDERSTOOD IN THIS INSTANCE. DATA COLLECTED AT LOWER RESOLUTION WITH A LOWER DOSE DID NOT SHOW THE SAME DISTORTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.11 3685 5 %RANDOM
Rwork0.1 ---
obs0.1 69370 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1→18.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms817 0 27 220 1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022968
X-RAY DIFFRACTIONr_bond_other_d0.0060.02847
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.951341
X-RAY DIFFRACTIONr_angle_other_deg1.91932005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13828.15838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73415157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.370.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021164
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02171
X-RAY DIFFRACTIONr_nbd_refined0.2820.2182
X-RAY DIFFRACTIONr_nbd_other0.1910.2848
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2514
X-RAY DIFFRACTIONr_nbtor_other0.0910.2673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6021.5649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.30621052
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1663344
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1254.5288
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
Rfree0.237 237
Rwork0.241 5011

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