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- PDB-2yc1: Crystal structure of the human derived single chain antibody frag... -

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Basic information

Entry
Database: PDB / ID: 2yc1
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: 1.9 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 10, 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,95015
Polymers71,1216
Non-polymers8299
Water10,233568
1
A: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
B: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
C: BETA-MAMMAL TOXIN CN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9297
Polymers35,5603
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-15.3 kcal/mol
Surface area13330 Å2
MethodPISA
2
D: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
E: SINGLE CHAIN ANTIBODY FRAGMENT 9004G
F: BETA-MAMMAL TOXIN CN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0218
Polymers35,5603
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-14.8 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.709, 219.709, 219.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11D-2027-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0007, -0.0004, -1), (-0.0003, -1, 0.0004), (-1, 0.0003, -0.0007)-54.8932, 54.9152, -54.9396
2given(-0.0002, -0.001, -1), (0.0014, -1, 0.001), (-1, -0.0014, 0.0002)-54.8886, 54.9137, -54.8892
3given(0.0011, 0.0006, -1), (-0.0004, -1, -0.0006), (-1, 0.0004, -0.0011)-54.95, 54.8897, -54.9529

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Components

#1: Antibody SINGLE CHAIN ANTIBODY FRAGMENT 9004G


Mass: 12533.847 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN
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.: 2 / Fragment: LIGHT CHAIN
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.: 2 / Source method: isolated from a natural source
Source: (natural) CENTRUROIDES NOXIUS HOFFMANN (Mexican scorpion)
References: UniProt: P01495
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 3.11 Å3/Da / Density % sol: 60.5 % / Description: NONE
Crystal growpH: 5.6 / Details: 1.4 M SODIUM / POTASSIUM PHOSPHATE PH 5.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 27, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→54.94 Å / Num. obs: 68864 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / % 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: PDB ENTRY 2YBR

2ybr


Resolution: 1.9→42.28 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21212 3488 5.1 %RANDOM
Rwork0.18613 ---
obs0.18743 65369 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: 24.649 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 54 568 5094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224703
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9586373
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5323.238210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47615756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1231536
X-RAY DIFFRACTIONr_chiral_restr0.0790.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213592
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_it3.7131.52894
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.93624632
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.77131809
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.6954.51727
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: 1.9→1.949 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.266 264 -
Rwork0.231 4844 -
obs--100 %

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