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- PDB-1a8d: TETANUS TOXIN C FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1a8d
TitleTETANUS TOXIN C FRAGMENT
ComponentsTETANUS NEUROTOXINTetanospasmin
KeywordsNEUROTOXIN / CLOSTRIDIAL / GANGLIOSIDE BINDING REGION
Function / homology
Function and homology information


tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding ...tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / COMBINED MIR (SIRAS), MAD INITIAL REFINEMENT WITH REFMAC, X-PLOR. FINAL REFINEMENT WITH SHELXL. / Resolution: 1.57 Å
AuthorsKnapp, M. / Rupp, B.
CitationJournal: Am.Cryst.Assoc.,Abstr.Papers (Annual Meeting) / Year: 1998
Title: The 1.61 Angstrom Structure of the Tetanus Toxin Ganglioside Binding Region: Solved by MAD and Mir Phase Combination
Authors: Knapp, M. / Segelke, B. / Rupp, B.
History
DepositionMar 23, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TETANUS NEUROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2203
Polymers51,8261
Non-polymers3942
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.180, 79.380, 93.810
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 TETANUS NEUROTOXIN / Tetanospasmin


Mass: 51826.426 Da / Num. of mol.: 1 / Fragment: C-FRAGMENT / Mutation: INS(M1)
Source method: isolated from a genetically manipulated source
Details: GOLD (AU) DERIVATIVE / Source: (gene. exp.) Clostridium tetani (bacteria)
Description: RECOMBINANT PROTEIN, PURCHASED FROM BOEHRINGER-MANNHEIM CATALOG NUMBER 1348-655
Production host: Escherichia coli (E. coli) / References: UniProt: P04958, tentoxilysin
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growMethod: fiber seeding using cryshed initial crystals as seeds
pH: 7
Details: 9% (W/V) 1M AMMONIUM PHOSPHATE, PH 6.0, AND 92% OF A 10% (W/V) SOLUTION OF PEG 6000 IN 50MM HEPES (PH 7.0). LARGE CRYSTALS (0.2 X 0.2 X 0.5 MM) WERE GROWN BY FIBER SEEDING, USING CRUSHED ...Details: 9% (W/V) 1M AMMONIUM PHOSPHATE, PH 6.0, AND 92% OF A 10% (W/V) SOLUTION OF PEG 6000 IN 50MM HEPES (PH 7.0). LARGE CRYSTALS (0.2 X 0.2 X 0.5 MM) WERE GROWN BY FIBER SEEDING, USING CRUSHED INITIAL CRYSTALS AS SEEDS., fiber seeding using cryshed initial crystals as seeds
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0396
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Dec 1, 1997 / Details: SLITS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
ReflectionHighest resolution: 1.57 Å / Num. obs: 72263 / % possible obs: 96.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.0569 / Net I/σ(I): 9.6
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.05 / % possible all: 90.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97model building
SOLVEphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
SHELXL-97phasing
RefinementMethod to determine structure: COMBINED MIR (SIRAS), MAD INITIAL REFINEMENT WITH REFMAC, X-PLOR. FINAL REFINEMENT WITH SHELXL.
Resolution: 1.57→22.5 Å / Num. parameters: 36750 / Num. restraintsaints: 45026 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.07 (7%)
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 7306 10.1 %RANDOM
all0.1867 72263 --
obs0.1785 -96.6 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4082.4
Refinement stepCycle: LAST / Resolution: 1.57→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 2 424 4083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.086

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