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- PDB-1sb2: High resolution Structure determination of rhodocetin -

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Basic information

Entry
Database: PDB / ID: 1sb2
TitleHigh resolution Structure determination of rhodocetin
Components
  • Rhodocetin alpha subunit
  • Rhodocetin beta subunit
KeywordsTOXIN / C-type lectin / domain swapping
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
: / 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
Snaclec rhodocetin subunit alpha / Snaclec rhodocetin subunit beta
Similarity search - Component
Biological speciesCalloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPaaventhan, P. / Kong, C.G. / Joseph, J.S. / Chung, M.C.M. / Kolatkar, P.R.
CitationJournal: Protein Sci. / Year: 2005
Title: Structure of rhodocetin reveals noncovalently bound heterodimer interface
Authors: Paaventhan, P. / Kong, C.G. / Joseph, J.S. / Chung, M.C.M. / Kolatkar, P.R.
History
DepositionFeb 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodocetin alpha subunit
B: Rhodocetin beta subunit


Theoretical massNumber of molelcules
Total (without water)31,1962
Polymers31,1962
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-20 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.875, 65.935, 118.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Rhodocetin alpha subunit


Mass: 15982.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: organism name synonym: Agkistrodon rhodostoma
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: P81397
#2: Protein Rhodocetin beta subunit


Mass: 15213.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: organism name synonym: Agkistrodon rhodostoma
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: P81398
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaH2PO4, KH2PO4, HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.978569 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 2001 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978569 Å / Relative weight: 1
ReflectionResolution: 1.9→28.87 Å / Num. all: 28995 / Num. obs: 27466 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 78.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.87 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.226 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.13
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23139 1472 5.1 %RANDOM
Rwork0.18918 ---
all0.19128 28995 --
obs0.19128 27466 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.568 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2104 0 0 167 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212168
X-RAY DIFFRACTIONr_bond_other_d0.0020.021837
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.932925
X-RAY DIFFRACTIONr_angle_other_deg0.99834314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1565253
X-RAY DIFFRACTIONr_chiral_restr0.1750.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022388
X-RAY DIFFRACTIONr_gen_planes_other0.010.02468
X-RAY DIFFRACTIONr_nbd_refined0.2360.2421
X-RAY DIFFRACTIONr_nbd_other0.2570.22097
X-RAY DIFFRACTIONr_nbtor_other0.0890.21174
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.25
X-RAY DIFFRACTIONr_mcbond_it1.1831.51274
X-RAY DIFFRACTIONr_mcangle_it2.1822042
X-RAY DIFFRACTIONr_scbond_it3.1273894
X-RAY DIFFRACTIONr_scangle_it4.8324.5883
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 73
Rwork0.236 1572

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