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- PDB-1f0l: 1.55 ANGSTROM CRYSTAL STRUCTURE OF WILD TYPE DIPHTHERIA TOXIN -

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Basic information

Entry
Database: PDB / ID: 1f0l
Title1.55 ANGSTROM CRYSTAL STRUCTURE OF WILD TYPE DIPHTHERIA TOXIN
ComponentsDIPHTHERIA TOXIN
KeywordsTOXIN / BACTERIAL TOXIN / ADP-RIBOSYLATION / TRANSMEMBRANE
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Uptake and function of diphtheria toxin / protein transmembrane transporter activity / nucleotidyltransferase activity / toxin activity / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain ...Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Globin-like / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE / Diphtheria toxin
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSteere, B. / Eisenberg, D.
CitationJournal: Thesis / Year: 2001
Title: Characterization of High-Order Oligomerization and Energetics in Diphtheria Toxin
Authors: Steere, B.
History
DepositionMay 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET R1 IS NOT A CLOSED BARREL, BUT IT IS CLOSED ON ONE SIDE AND FLATTENED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN
B: DIPHTHERIA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,44913
Polymers116,8232
Non-polymers1,62611
Water32,5891809
1
A: DIPHTHERIA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2076
Polymers58,4111
Non-polymers7955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DIPHTHERIA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2427
Polymers58,4111
Non-polymers8316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.770, 134.880, 46.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999517, -0.030412, -0.006347), (-0.030473, 0.999489, 0.00967), (0.00605, 0.009858, -0.999933)
Vector: -67.24366, -2.1123, 93.34802)
DetailsTHERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT, INDICATED BY CHAIN IDENTIFIERS A AND B. THE NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATING A TO B IS SPECIFIED IN THE MTRIX RECORDS BELOW. THIS TRANSFORMATION WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A.

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Components

#1: Protein DIPHTHERIA TOXIN


Mass: 58411.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Corynebacterium diphtheriae (bacteria) / References: UniProt: P00588
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-APU / ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE


Mass: 653.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N7O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1809 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 MICROLITERS OF PROTEIN SOLUTION CONSISTING OF: 8 MG/ML WILD TYPE DIPHTHERIA TOXIN MONOMER + APUP, 0.5 MILLIMOLAR EDTA, 50 MILLIMOLAR TRIS-HCL, PH 7.5 PLUS 2 MICROLITERS OF RESERVIOR ...Details: 2 MICROLITERS OF PROTEIN SOLUTION CONSISTING OF: 8 MG/ML WILD TYPE DIPHTHERIA TOXIN MONOMER + APUP, 0.5 MILLIMOLAR EDTA, 50 MILLIMOLAR TRIS-HCL, PH 7.5 PLUS 2 MICROLITERS OF RESERVIOR SOLUTION CONSISTING OF: 17% PEG 8000, 1 MOLAR SODIUM CHLORIDE, 50 MILLIMOLAR TRIS-HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. all: 583084 / Num. obs: 149412 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 6.8
Reflection shellResolution: 1.55→1.62 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.5 / Num. unique all: 18092 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXLrefinement
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MDT

1mdt


Resolution: 1.55→40 Å / Num. parameters: 41198 / Num. restraintsaints: 35383 / Cross valid method: FREE R / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: Used conjugate gradient least squares procedure Model refined using I's, not F's Riding hydrogens placed on protein atoms with HFIX
RfactorNum. reflection% reflectionSelection details
Rfree0.238 7212 4 %NCS-RELATED (G.PFLUEGL)
Rwork0.188 ---
all0.188 149412 --
obs0.188 149412 97 %-
Solvent computationSolvent model: Moews and Kretsinger, J.Mol.Biol. 91(1973) 201-228
Refine analyzeNum. disordered residues: 78 / Occupancy sum hydrogen: 7782 / Occupancy sum non hydrogen: 9442
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8300 0 95 1809 10204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0256
X-RAY DIFFRACTIONs_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.039
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps0

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