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- PDB-2ybr: Crystal structure of the human derived single chain antibody frag... -

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Basic information

Entry
Database: PDB / ID: 2ybr
TitleCrystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann
Components
  • (SINGLE CHAIN ANTIBODY FRAGMENT 9004G) x 2
  • BETA-MAMMAL TOXIN CN2
KeywordsIMMUNE SYSTEM/TOXIN / IMMUNE SYSTEM-TOXIN COMPLEX / SCORPION TOXIN
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-mammal toxin Cn2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
CENTRUROIDES NOXIUS HOFFMANN (Mexican scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsCanul-Tec, J.C. / Riano-Umbarila, L. / Rudino-Pinera, E. / Becerril, B. / Possani, L.D. / Torres-Larios, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides Noxius Hoffmann by a Human-Derived Single Chain Antibody Fragment
Authors: Canul-Tec, J.C. / Riano-Umbarila, L. / Rudino-Pinera, E. / Becerril, B. / Possani, L.D. / Torres-Larios, A.
History
DepositionMar 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 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: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
B: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
C: BETA-MAMMAL TOXIN CN2
D: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
E: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
F: BETA-MAMMAL TOXIN CN2
G: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
H: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
I: BETA-MAMMAL TOXIN CN2


Theoretical massNumber of molelcules
Total (without water)106,6819
Polymers106,6819
Non-polymers00
Water3,963220
1
A: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
B: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
C: BETA-MAMMAL TOXIN CN2


Theoretical massNumber of molelcules
Total (without water)35,5603
Polymers35,5603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-15.9 kcal/mol
Surface area13430 Å2
MethodPISA
2
D: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
E: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
F: BETA-MAMMAL TOXIN CN2


Theoretical massNumber of molelcules
Total (without water)35,5603
Polymers35,5603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-14.3 kcal/mol
Surface area13120 Å2
MethodPISA
3
G: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
H: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
I: BETA-MAMMAL TOXIN CN2


Theoretical massNumber of molelcules
Total (without water)35,5603
Polymers35,5603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-13.3 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.844, 104.494, 152.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9994, -0.0113, 0.0319), (0.0218, 0.5047, 0.863), (-0.0259, 0.8632, -0.5041)-35.0027, -9.1771, 24.4139
2given(-0.9986, -0.0082, 0.0531), (0.0503, -0.4907, 0.8699), (0.0189, 0.8713, 0.4904)-71.3242, -20.6686, 14.8426
3given(-0.9995, -0.0212, 0.0214), (0.0074, 0.5186, 0.855), (-0.0292, 0.8548, -0.5182)-34.8269, -9.6341, 24.4174
4given(-0.9998, -0.007, 0.0185), (0.0195, -0.4948, 0.8688), (0.0031, 0.869, 0.4948)-70.1488, -22.1178, 13.8823
5given(-0.999, 0.0129, -0.043), (-0.031, 0.4938, 0.869), (0.0324, 0.8695, -0.4929)-36.0636, -9.9119, 25.6794
6given(-0.9996, -0.0023, 0.0276), (0.025, -0.5023, 0.8643), (0.0119, 0.8647, 0.5022)-70.4167, -21.5566, 14.17

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Components

#1: Antibody SINGLE CHAIN ANTIBODY FRAGMENT 9004G


Mass: 12533.847 Da / Num. of mol.: 3 / Fragment: HEAVY CHAIN, RESIDUES 1-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1
#2: Antibody SINGLE CHAIN ANTIBODY FRAGMENT 9004G


Mass: 15418.860 Da / Num. of mol.: 3 / Fragment: LIGHT CHAIN, RESIDUES 118-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSYN1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1
#3: Protein BETA-MAMMAL TOXIN CN2 / CN2 TOXIN / TOXIN 2 / TOXIN II.9.2.2


Mass: 7607.728 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) CENTRUROIDES NOXIUS HOFFMANN (Mexican scorpion)
References: UniProt: P01495
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.61 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 5.5
Details: 100 MM BIS-TRIS, PH 5.5, 25% PEG 3350 AND 200 MM (NH4)2SO4.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Nov 6, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→46.2 Å / Num. obs: 37179 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON PDB ENTRIES 1CN2, 1QLR, AND 1DFB

1cn2

1qlr

1dfb


Resolution: 2.55→45.72 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.478 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24673 1858 5 %RANDOM
Rwork0.19183 ---
obs0.19455 35277 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.766 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--0.63 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6721 0 0 220 6941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226886
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.959318
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90123.17306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.996151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1441552
X-RAY DIFFRACTIONr_chiral_restr0.0780.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3441.54295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.70226838
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.18432591
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1554.52480
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.323 130 -
Rwork0.305 2577 -
obs--100 %

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