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- PDB-1wvr: Crystal Structure of a CRISP family Ca-channel blocker derived fr... -

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Basic information

Entry
Database: PDB / ID: 1wvr
TitleCrystal Structure of a CRISP family Ca-channel blocker derived from snake venom
ComponentsTriflin
KeywordsTOXIN / cysteine-rich secretory protein
Function / homology
Function and homology information


calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related ...Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain / ShKT domain profile. / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Cysteine-rich venom protein triflin
Similarity search - Component
Biological speciesTrimeresurus flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crysatl 2 MAD PROTOCOL / Resolution: 2.4 Å
AuthorsShikamoto, Y. / Suto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a CRISP family Ca2+ -channel blocker derived from snake venom.
Authors: Shikamoto, Y. / Suto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H.
#1: Journal: Eur.J.Biochem. / Year: 2002
Title: Cloning and characterization of novel snake venom proteins that block smooth muscle contraction
Authors: Yamazaki, Y. / Koike, H. / Sugiyama, Y. / Motoyoshi, K. / Wada, T. / Hishinuma, S. / Mita, M. / Morita, T.
#2: Journal: Arch.Biochem.Biophys. / Year: 2003
Title: Wide distribution of cysteine-rich secretory proteins in snake venoms: isolation and cloning of novel snake venom cysteine-rich secretory proteins
Authors: Yamazaki, Y. / Hyodo, F. / Morita, T.
History
DepositionDec 24, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triflin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,83910
Polymers24,8271
Non-polymers1,0129
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Triflin
hetero molecules

A: Triflin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,67720
Polymers49,6542
Non-polymers2,02318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4230 Å2
ΔGint-119 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.374, 83.374, 85.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Triflin


Mass: 24826.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Strain: Tokunoshima / References: UniProt: Q8JI39
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-HCl, PEG 400, sodium acetate, sodium cadmium, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11.0403
21.0403, 1.0406, 1.0457
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 2002 / Details: mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1siliconSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.04031
21.04061
31.04571
ReflectionResolution: 2.3→38.11 Å / Num. all: 14053 / Num. obs: 13969 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 8.25
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1965 / Rsym value: 0.48 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crysatl 2 MAD PROTOCOL
Resolution: 2.4→38.11 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1353400.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 609 5 %RANDOM
Rwork0.227 ---
obs0.227 12235 99.2 %-
all-13844 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6302 Å2 / ksol: 0.329866 e/Å3
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.57 Å20 Å20 Å2
2--9.57 Å20 Å2
3----19.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 9 140 1883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 95 4.8 %
Rwork0.3 1899 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ACT.PARAMACT.TOP

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