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- PDB-1y62: A 2.4 crystal structure of conkunitzin-S1, a novel Kunitz-fold co... -

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Basic information

Entry
Database: PDB / ID: 1y62
TitleA 2.4 crystal structure of conkunitzin-S1, a novel Kunitz-fold cone snail neurotoxin.
ComponentsConkunitzin-S1
KeywordsTOXIN / alpha helix / beta sheet / 310 helix / Kunitz fold
Function / homology
Function and homology information


potassium channel regulator activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular region
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Kunitz-type conkunitzin-S1
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDy, C.Y. / Buczek, P. / Horvath, M.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of conkunitzin-S1, a neurotoxin and Kunitz-fold disulfide variant from cone snail.
Authors: Dy, C.Y. / Buczek, P. / Imperial, J.S. / Bulaj, G. / Horvath, M.P.
History
DepositionDec 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conkunitzin-S1
B: Conkunitzin-S1
C: Conkunitzin-S1
D: Conkunitzin-S1
E: Conkunitzin-S1
F: Conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,10921
Polymers41,6686
Non-polymers1,44115
Water93752
1
A: Conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1373
Polymers6,9451
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3295
Polymers6,9451
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0412
Polymers6,9451
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2334
Polymers6,9451
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2334
Polymers6,9451
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Conkunitzin-S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1373
Polymers6,9451
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.756, 51.543, 51.600
Angle α, β, γ (deg.)119.92, 107.52, 91.14
Int Tables number1
Space group name H-MP1
DetailsEach chain represents one biological unit.

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Components

#1: Protein
Conkunitzin-S1


Mass: 6944.685 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: The sequence of this peptide occurs naturally in Conus striatus (cone snail). This peptide was synthesized in two parts and subsequently joined through native chemical ligation.
References: UniProt: P0C1X2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG-400, ammonium sulfate, sodium azide, acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Aug 18, 2004 / Details: Nonius FR591 High brilliance
RadiationMonochromator: Osmic MaxFlux (Green) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 15511 / Num. obs: 15238 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.098
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1498 / Rsym value: 0.365 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble of the kunitz domains in 1DTX,1KNT, 2PTC and 1TFX

1dtx

1knt

2ptc

1tfx


Resolution: 2.45→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 122859.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1208 7.9 %RANDOM, 8%
Rwork0.221 ---
all0.232 15511 --
obs0.232 15238 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.8714 Å2 / ksol: 0.4066 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 75 52 2821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it2.742
X-RAY DIFFRACTIONc_scangle_it3.892.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.45-2.540.3271097.90.29692221149897.8
2.54-2.640.30031280.2661151798.7
2.64-2.760.31051150.2591151198.9
2.76-2.90.27371270.2382153299.2
2.9-3.080.28291260.2452152999
3.08-3.320.26351322222153499
3.32-3.650.27811130.2298153599
3.65-4.180.21021080.1999151199.3
4.18-5.250.21371270.1974154399.5
5.25-200.25751230.2582152899.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMION.TOP

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