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- PDB-1rc9: Crystal Structure of Stecrisp, a Member of CRISP Family from Trim... -

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Basic information

Entry
Database: PDB / ID: 1rc9
TitleCrystal Structure of Stecrisp, a Member of CRISP Family from Trimeresurus Stejnegeri Refined at 1.6 Angstroms Resolution: Structual relationship of the two domains
Componentscysteine-rich secretory protein
KeywordsTOXIN / beta-alpha sandwich / double domains / short helixs motif
Function / homology
Function and homology information


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 / Cysteine-rich secretory protein family / CAP superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cysteine-rich venom protein
Similarity search - Component
Biological speciesViridovipera stejnegeri (Stejneger's pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsGuo, M. / Teng, M. / Niu, L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of cysteine-rich secretory protein stecrisp reveals the cysteine-rich domain has a K+-channel inhibitor-like fold.
Authors: Guo, M. / Teng, M. / Niu, L. / Liu, Q. / Huang, Q. / Hao, Q.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 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: cysteine-rich secretory protein


Theoretical massNumber of molelcules
Total (without water)25,1531
Polymers25,1531
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.381, 78.421, 106.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-398-

HOH

21A-411-

HOH

31A-444-

HOH

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Components

#1: Protein cysteine-rich secretory protein / stecrisp


Mass: 25153.078 Da / Num. of mol.: 1 / Fragment: residue 13-233 / Source method: isolated from a natural source
Source: (natural) Viridovipera stejnegeri (Stejneger's pit viper)
Organ: venom gland / References: UniProt: P60623
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: PEG 4000, sodium acetate, Tris-HCl, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.9363
SYNCHROTRONBSRF 3W1A21.75
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 1, 2003
MARRESEARCH2IMAGE PLATEJul 1, 2003
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93631
21.751
ReflectionResolution: 1.6→33 Å / Num. all: 34039 / Num. obs: 34039 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.28 / Num. unique all: 1571 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
MAR345data collection
SCALEPACKdata scaling
AUTOMARdata reduction
SHELXphasing
SHARPphasing
DMphasing
SOLOMONphasing
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→32.37 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2655338.29 / Data cutoff high rms absF: 2655338.29 / 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
Rfree0.219 3399 10 %RANDOM
Rwork0.192 ---
all0.192 34039 --
obs0.192 34039 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0572 Å2 / ksol: 0.404396 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-33 Å
Luzzati sigma a0.16 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 0 225 1981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 328 10.1 %
Rwork0.304 2918 -
obs-3247 95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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