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- PDB-1c3a: CRYSTAL STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM, A NO... -

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Basic information

Entry
Database: PDB / ID: 1c3a
TitleCRYSTAL STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM, A NOVEL CYCLIC TETRAMER OF C-TYPE LECTIN-LIKE HETERODIMERS
Components
  • FLAVOCETIN-A: ALPHA SUBUNIT
  • FLAVOCETIN-A: BETA SUBUNIT
KeywordsMEMBRANE PROTEIN / C-TYPE LECTIN-LIKE DOMAINS
Function / homology
Function and homology information


toxin activity / extracellular region
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, 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
Snaclec flavocetin-A subunit alpha / Snaclec flavocetin-A subunit beta
Similarity search - Component
Biological speciesTrimeresurus flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFukuda, K. / Mizuno, H. / Atoda, H. / Morita, T.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of flavocetin-A, a platelet glycoprotein Ib-binding protein, reveals a novel cyclic tetramer of C-type lectin-like heterodimers.
Authors: Fukuda, K. / Mizuno, H. / Atoda, H. / Morita, T.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 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: FLAVOCETIN-A: ALPHA SUBUNIT
B: FLAVOCETIN-A: BETA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)30,2312
Polymers30,2312
Non-polymers00
Water1,67593
1
A: FLAVOCETIN-A: ALPHA SUBUNIT
B: FLAVOCETIN-A: BETA SUBUNIT

A: FLAVOCETIN-A: ALPHA SUBUNIT
B: FLAVOCETIN-A: BETA SUBUNIT

A: FLAVOCETIN-A: ALPHA SUBUNIT
B: FLAVOCETIN-A: BETA SUBUNIT

A: FLAVOCETIN-A: ALPHA SUBUNIT
B: FLAVOCETIN-A: BETA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)120,9238
Polymers120,9238
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-20 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.510, 120.510, 62.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a tetramer made up of four identical heterodimers related by a crystallographic fourfold symmetry parallel to the c-axis.

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Components

#1: Protein FLAVOCETIN-A: ALPHA SUBUNIT


Mass: 15667.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRIMERESURUS FLAVOVIRIDIS / Source: (natural) Trimeresurus flavoviridis (habu) / References: UniProt: Q8AV97
#2: Protein FLAVOCETIN-A: BETA SUBUNIT


Mass: 14563.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRIMERESURUS FLAVOVIRIDIS / Source: (natural) Trimeresurus flavoviridis (habu) / References: UniProt: Q8AV98
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2-methyl-2,4-pentanediol, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 67 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 %(v/v)MPD1reservoir
20.1 Msodium acetate1reservoir
310 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→85 Å / Num. all: 15775 / Num. obs: 15078 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.61 Å / Rmerge(I) obs: 0.377 / Num. unique all: 1467 / % possible all: 74.2
Reflection shell
*PLUS
% possible obs: 74.2 % / Rmerge(I) obs: 0.38

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.5→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 555 5 %RANDOM
Rwork0.208 ---
obs0.208 11391 74.3 %-
all-13893 --
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 0 93 2217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_improper_angle_d1
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 -5 %
Rwork0.329 553 -
obs--30.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19X.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1

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