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- PDB-1xta: Crystal Structure of Natrin, a snake venom CRISP from Taiwan cobr... -

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Basic information

Entry
Database: PDB / ID: 1xta
TitleCrystal Structure of Natrin, a snake venom CRISP from Taiwan cobra (Naja atra)
ComponentsNatrin 1
KeywordsTOXIN / natrin / CRISP / serine protease / ion channel blocking / naja atra / cobra
Function / homology
Function and homology information


calcium channel regulator activity / potassium 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 / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain ...Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / 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 natrin-1
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsWang, Y.-L. / Goh, K.-X. / Lee, S.-C. / Huang, W.-N. / Wu, W.-G. / Chen, C.-J.
Citation
Journal: To be Published
Title: Structures of snake venom CRISP reveal an action mechanism involving serine protease and ion channel blocking domains
Authors: Wang, Y.-L. / Goh, K.-X. / Lee, S.-C. / Huang, W.-N. / Wu, W.-G. / Chen, C.-J.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray crystallographic analysis of a cysteine-rich secretory protein (CRISP) from Naja atra venom
Authors: Wang, Y.-L. / Goh, K.-X. / Wu, W.-G. / Chen, C.-J.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natrin 1
B: Natrin 1


Theoretical massNumber of molelcules
Total (without water)49,9082
Polymers49,9082
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.127, 64.985, 242.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer generated from NCS in the asymmetric unit

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Components

#1: Protein Natrin 1 / Cysteine-rich venom protein 1 / NA-CRVP1 / CRISP


Mass: 24954.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: Q7T1K6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG6000, ammonium citrate, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL17B211.743
SYNCHROTRONSPring-8 BL12B221
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDAug 15, 2004
ADSC QUANTUM 4r2CCDAug 30, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.7431
211
ReflectionResolution: 1.58→25 Å / Num. all: 61378 / Num. obs: 59203 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.86 %
Reflection shellResolution: 1.58→1.64 Å / % possible all: 83.7

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Processing

Software
NameVersionClassification
ADSCdata collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.58→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 5686 RANDOM
Rwork0.223 --
all0.236 61378 -
obs0.228 59203 -
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.12 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 0 267 3732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.427

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