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- PDB-2epf: Crystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus -

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Basic information

Entry
Database: PDB / ID: 2epf
TitleCrystal Structure of Zinc-Bound Pseudecin From Pseudechis Porphyriacus
ComponentsPseudecin
KeywordsTOXIN / CRISP / SNAKE VENOM / CNG CHANNEL
Function / homology
Function and homology information


ion channel regulator activity / toxin activity / extracellular space / 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 / 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 pseudecin
Similarity search - Component
Biological speciesPseudechis porphyriacus (red-bellied black snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMar 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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_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: Pseudecin
B: Pseudecin
C: Pseudecin
D: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,88512
Polymers94,4894
Non-polymers3968
Water3,531196
1
A: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7764
Polymers23,6221
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6882
Polymers23,6221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7113
Polymers23,6221
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7113
Polymers23,6221
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Pseudecin
hetero molecules

D: Pseudecin
hetero molecules

B: Pseudecin
C: Pseudecin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,88512
Polymers94,4894
Non-polymers3968
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_465x-1,y+1,z1
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-242.6 kcal/mol
Surface area36250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.077, 62.344, 246.943
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
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, 3MM ZN ACETATE, 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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42142 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.377 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3945 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DDB

2ddb


Resolution: 2.3→38.72 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.513 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27717 2122 5 %RANDOM
Rwork0.2186 ---
obs0.22156 39944 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--1.99 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 0 8 196 6700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9279120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24123.429280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.987151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3861536
X-RAY DIFFRACTIONr_chiral_restr0.0830.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025116
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.22966
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24534
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4851.54152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92926708
X-RAY DIFFRACTIONr_scbond_it1.30132717
X-RAY DIFFRACTIONr_scangle_it2.0974.52412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 132 -
Rwork0.25 2634 -
obs--100 %

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