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- PDB-1muq: X-ray Crystal Structure of Rattlesnake Venom Complexed With Thiod... -

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Basic information

Entry
Database: PDB / ID: 1muq
TitleX-ray Crystal Structure of Rattlesnake Venom Complexed With Thiodigalactoside
ComponentsGalactose-specific lectin
KeywordsSUGAR BINDING PROTEIN / C-type lectin / protein-carbohydrate complex / decamer / calcium binding
Function / homology
Function and homology information


signaling receptor activity / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
thiodigalactoside / beta-D-galactopyranose / C-type lectin Cal
Similarity search - Component
Biological speciesCrotalus atrox (western diamondback rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsWalker, J.R. / Nagar, B. / Young, N.M. / Hirama, T. / Rini, J.M.
Citation
Journal: Biochemistry / Year: 2004
Title: X-ray Crystal Structure of a Galactose-Specific C-Type Lectin Possessing a Novel Decameric Quaternary Structure.
Authors: Walker, J.R. / Nagar, B. / Young, N.M. / Hirama, T. / Rini, J.M.
#1: Journal: Biochem.J. / Year: 1984
Title: Isolation and characterization of three Ca2+-dependent beta-galactoside-specific lectins from snake venoms
Authors: Gartner, T.K. / Ogilvie, M.L.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Complete primary structure of a galactose-specific lectin from the venom of the rattlesnake Crotalus atrox. Homologies with Ca2(+)-dependent-type lectins
Authors: Hirabayashi, J.T. / Kusunoki, T. / Kasai, K.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_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_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Oct 14, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_molecule_features / pdbx_struct_conn_angle / struct_conn
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.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_asym_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_link.entity_branch_list_num_1 / _pdbx_entity_branch_link.entity_branch_list_num_2 / _pdbx_entity_branch_list.comp_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose-specific lectin
B: Galactose-specific lectin
C: Galactose-specific lectin
D: Galactose-specific lectin
E: Galactose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,77619
Polymers81,5625
Non-polymers1,21414
Water2,720151
1
A: Galactose-specific lectin
B: Galactose-specific lectin
C: Galactose-specific lectin
D: Galactose-specific lectin
E: Galactose-specific lectin
hetero molecules

A: Galactose-specific lectin
B: Galactose-specific lectin
C: Galactose-specific lectin
D: Galactose-specific lectin
E: Galactose-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,55238
Polymers163,12410
Non-polymers2,42828
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area19430 Å2
ΔGint-278 kcal/mol
Surface area57570 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.454, 151.234, 95.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a decamer generated from the pentamer in the asymetric unit by the two fold axis -x, -y, z+1/2

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Galactose-specific lectin / RSL (Rattlesnake Lectin)


Mass: 16312.377 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: Isolated from venom
Source: (natural) Crotalus atrox (western diamondback rattlesnake)
References: UniProt: P21963

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 1-thio-beta-D-galactopyranose-(1-1)-beta-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 358.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with reducing-end-to-reducing-end glycosidic bond
References: thiodigalactoside
DescriptorTypeProgram
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Galp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 161 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, glycerol, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
210 mMTris1droppH8.0
31 mM1dropCaCl2
4100 mMthiodigalactoside1drop
55 Msodium formate1reservoir
6100 mMHEPES1reservoirpH7.0
710 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.909 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1998
RadiationMonochromator: horizontally focussing, 5.05 degrees asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 2.2→35.13 Å / Num. all: 40555 / Num. obs: 40555 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.37
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.42 / Num. unique all: 1653 / % possible all: 82.9
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. obs: 33477
Reflection shell
*PLUS
% possible obs: 82.9 % / Rmerge(I) obs: 0.402

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2.3→35.13 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3277247.32 / Data cutoff high rms absF: 3277247.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Positions of sulfer atoms contributing to the disulfide bond between pentamers were fixed during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3323 9.9 %RANDOM
Rwork0.21 ---
all0.21 33477 --
obs0.21 33477 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2996 Å2 / ksol: 0.439546 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20 Å2
2---4.65 Å20 Å2
3---7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 69 151 5910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it3.571.5
X-RAY DIFFRACTIONc_mcangle_it5.272
X-RAY DIFFRACTIONc_scbond_it5.812
X-RAY DIFFRACTIONc_scangle_it7.972.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 554 10.7 %
Rwork0.28 4623 -
obs-4623 88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE_PLNG.PARAM
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 35 Å / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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