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- PDB-1hq0: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF E.COLI CYTOTOXIC NEC... -

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Basic information

Entry
Database: PDB / ID: 1hq0
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF E.COLI CYTOTOXIC NECROTIZING FACTOR TYPE 1
ComponentsCYTOTOXIC NECROTIZING FACTOR 1
KeywordsTOXIN / BETA SANDWICH / RHO DEAMIDASE / RHO TRANSGLUTAMINASE
Function / homology
Function and homology information


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 / SYNCHROTRON / MAD / Resolution: 1.83 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
DepositionDec 13, 2000Deposition 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)32,9434
Polymers32,6581
Non-polymers2853
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.000, 55.000, 176.200
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: 32658.438 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: L794P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CNF1 / 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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.358 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium phosphate, potassium phosphate, 1,4-butanediol, 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSSRL BL1-520.97943, 0.980035, 0.925256, 1.06883
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEMar 28, 2000focusing mirrors
ADSC QUANTUM 42CCDApr 5, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic MirrorSINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.979431
30.9800351
40.9252561
51.068831
ReflectionResolution: 1.76→20 Å / Num. all: 29261 / Num. obs: 26431 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 20.7 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 26 / Limit k min: 0 / Limit l max: 99 / Limit l min: 0 / Observed criterion F max: 1515682.95 / Observed criterion F min: 7.5 / Rmerge(I) obs: 0.056 / Net I/σ(I): 36.7
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→20 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1306 4.9 %Random 5% of data
Rwork0.191 ---
all0.193 26457 --
obs0.193 26447 100 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 52.0432 Å2 / ksol: 0.336574 e/Å3
Displacement parametersBiso max: 79.96 Å2 / Biso mean: 28.05 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å21.98 Å20 Å2
2--2.93 Å20 Å2
3----5.85 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Luzzati d res high-1.83
Refinement stepCycle: LAST / Resolution: 1.83→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 15 204 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg25.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.69
X-RAY DIFFRACTIONx_mcbond_it2.483
X-RAY DIFFRACTIONx_mcangle_it3.484
X-RAY DIFFRACTIONx_scbond_it3.744
X-RAY DIFFRACTIONx_scangle_it4.785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.83-1.910.2621454.40.24731170.0223272326099.8
1.91-2.010.2111404.20.21231560.0183303329699.8
2.01-2.140.2071695.10.20631500.0163327331999.8
2.14-2.30.2061785.40.20431420.0153325332099.8
2.3-2.540.1951484.50.19431330.0163284328199.9
2.54-2.90.191735.20.18931570.01433313330100
2.9-3.650.1881935.80.18531240.01433183317100
3.65-19.990.1771604.80.17831640.01433243324100
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it3
X-RAY DIFFRACTIONc_scbond_it4
X-RAY DIFFRACTIONc_mcangle_it4
X-RAY DIFFRACTIONc_scangle_it5
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.247

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