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- PDB-1hzg: CRYSTAL STRUCTURE OF THE INACTIVE C866S MUTANT OF THE CATALYTIC D... -

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Basic information

Entry
Database: PDB / ID: 1hzg
TitleCRYSTAL STRUCTURE OF THE INACTIVE C866S MUTANT OF THE CATALYTIC DOMAIN OF E. COLI CYTOTOXIC NECROTIZING FACTOR 1
ComponentsCYTOTOXIC NECROTIZING FACTOR 1
KeywordsTOXIN / Beta Sandwich / Rho Deamidase / Rho Transglutaminase
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell-cell junction
Similarity search - Function
Cytotoxic necrotizing factor 1 (CNF1) / Cytotoxic necrotizing factor, Rho-activating domain / Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic ...Cytotoxic necrotizing factor 1 (CNF1) / Cytotoxic necrotizing factor, Rho-activating domain / Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cytotoxic necrotizing factor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Difference Fourier / Resolution: 1.86 Å
AuthorsBuetow, L. / Flatau, G. / Chiu, K. / Boquet, P. / Ghosh, P.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the Rho-activating domain of Escherichia coli cytotoxic necrotizing factor 1.
Authors: Buetow, L. / Flatau, G. / Chiu, K. / Boquet, P. / Ghosh, P.
History
DepositionJan 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOTOXIC NECROTIZING FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8323
Polymers32,6421
Non-polymers1902
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.900, 54.900, 176.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein CYTOTOXIC NECROTIZING FACTOR 1 / CNF1


Mass: 32642.375 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: C866S, L794P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: E-B35 / Plasmid: PET 28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47106
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium phosphate, potassium phosphate, 1,4-butandiol, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.65 Msodium phosphate1reservoir
20.65 Mpotassium phosphate1reservoir
3100 mMHEPES1reservoir
45 %(v/v)1,4-butanediol1reservoir
52 mMdithiothreitol1reservoir
6150 mM1dropNaCl
720 mMTris1drop
82 mMdithiothreitol1drop
915 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-5 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 4, 2000 / Details: Supper mirror
RadiationMonochromator: Supper mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→15 Å / Num. all: 25165 / Num. obs: 25142 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 33.8
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 3.5 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 15 Å

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Difference Fourier
Starting model: PDB Entry 1HQ0

1hq0


Resolution: 1.86→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1444667.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Maximum Likelihood Refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1241 4.9 %RANDOM
Rwork0.198 ---
all0.2 ---
obs0.2 25152 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.38 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å22.61 Å20 Å2
2--3.36 Å20 Å2
3----6.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.86→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 10 157 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 166 4 %
Rwork0.258 4011 -
obs-4011 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PHOSPHATE.PARAMPHOSPHATE.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.198 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 4 % / Rfactor Rwork: 0.258

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