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- PDB-2ddb: Crystal structure of pseudecin from Pseudechis porphyriacus -

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Basic information

Entry
Database: PDB / ID: 2ddb
TitleCrystal structure of pseudecin from Pseudechis porphyriacus
ComponentsPseudecin
KeywordsTOXIN / CRISP / snake venom / CNG channel
Function / homology
Function and homology information


ion channel regulator activity / toxin activity / extracellular region / metal ion binding
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 / 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
FORMIC ACID / Cysteine-rich venom protein pseudecin
Similarity search - Component
Biological speciesPseudechis porphyriacus (red-bellied black snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSuzuki, N. / Yamazaki, Y. / Fujimoto, Z. / Morita, T. / Mizuno, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain
Authors: Suzuki, N. / Yamazaki, Y. / Brown, R.L. / Fujimoto, Z. / Morita, T. / Mizuno, H.
History
DepositionJan 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudecin
B: Pseudecin
C: Pseudecin
D: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,10035
Polymers94,4894
Non-polymers1,61131
Water12,989721
1
A: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,24412
Polymers23,6221
Non-polymers62111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7374
Polymers23,6221
Non-polymers1153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,10611
Polymers23,6221
Non-polymers48310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0148
Polymers23,6221
Non-polymers3917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.707, 61.668, 251.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pseudecin / Channel blocker


Mass: 23622.299 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Pseudechis porphyriacus (red-bellied black snake)
Tissue: venom / References: UniProt: Q8AVA3
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.6M sodium formate, 10%(w/v) glycerol, 0.15M NaCl, 50mM Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 74335 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7454 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WVR

1wvr


Resolution: 1.9→43.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.842 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3745 5 %RANDOM
Rwork0.206 ---
all0.209 ---
obs-74329 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.737 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 103 721 7356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226830
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9349223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54223.333282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.095151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2731538
X-RAY DIFFRACTIONr_chiral_restr0.0840.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025142
X-RAY DIFFRACTIONr_nbd_refined0.1980.23190
X-RAY DIFFRACTIONr_nbtor_refined0.30.24616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2619
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.232
X-RAY DIFFRACTIONr_mcbond_it0.5811.54214
X-RAY DIFFRACTIONr_mcangle_it1.07826740
X-RAY DIFFRACTIONr_scbond_it1.53732776
X-RAY DIFFRACTIONr_scangle_it2.4454.52483
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 271 -
Rwork0.267 5212 -
obs-5483 100 %

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