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- PDB-4fxq: Full-length Certhrax toxin from Bacillus cereus in complex with I... -

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Basic information

Entry
Database: PDB / ID: 4fxq
TitleFull-length Certhrax toxin from Bacillus cereus in complex with Inhibitor P6
ComponentsPutative ADP-ribosyltransferase Certhrax
KeywordsTOXIN / TRANSFERASE/TRANSFERASE INHIBITOR / mixed alpha/beta / mono-adp-ribosyltransferase / BACTERIAL TOXIN / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / metallopeptidase activity / toxin activity / nucleotide binding / extracellular region / metal ion binding
Similarity search - Function
Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. ...Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-G9L / Putative ADP-ribosyltransferase Certhrax
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9599 Å
AuthorsVisschedyk, D.D. / Dimov, S. / Kimber, M.S. / Park, H.W. / Merrill, A.R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Certhrax Toxin, an Anthrax-related ADP-ribosyltransferase from Bacillus cereus.
Authors: Visschedyk, D. / Rochon, A. / Tempel, W. / Dimov, S. / Park, H.W. / Merrill, A.R.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ADP-ribosyltransferase Certhrax
B: Putative ADP-ribosyltransferase Certhrax
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0169
Polymers107,1482
Non-polymers8677
Water8,881493
1
A: Putative ADP-ribosyltransferase Certhrax
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0265
Polymers53,5741
Non-polymers4514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ADP-ribosyltransferase Certhrax
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9904
Polymers53,5741
Non-polymers4163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.310, 100.290, 191.090
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 Putative ADP-ribosyltransferase Certhrax / Toxin Certhrax


Mass: 53574.195 Da / Num. of mol.: 2 / Fragment: UNP Residues 18-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: G9241
Gene: Amino acids 18-471, BCE_G9241_pBC218_0027, pBC218_0027
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4MV79, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-G9L / 8-fluoro-2-(3-piperidin-1-ylpropanoyl)-1,3,4,5-tetrahydrobenzo[c][1,6]naphthyridin-6(2H)-one


Mass: 357.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24FN3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 2.4 M sodium malonate, 10 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2011
RadiationMonochromator: Double Crystal Monochromator (ACCEL DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9599→48.503 Å / Num. all: 84767 / Num. obs: 84731 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9599→2.03 Å / % possible all: 98

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
AutoProcess(XDSdata reduction
BESTdata reduction
pointlessbased automatic processing script)data scaling
XDSdata reduction
HKL-2000data reduction
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Certhrax full-length

Resolution: 1.9599→48.503 Å / SU ML: 0.24 / σ(F): 2 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 4236 5 %random
Rwork0.1874 ---
obs0.1894 84731 99.14 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.092 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4387 Å20 Å2-0 Å2
2--2.5762 Å20 Å2
3----3.015 Å2
Refinement stepCycle: LAST / Resolution: 1.9599→48.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 57 493 7846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077514
X-RAY DIFFRACTIONf_angle_d1.01210114
X-RAY DIFFRACTIONf_dihedral_angle_d13.6892896
X-RAY DIFFRACTIONf_chiral_restr0.0741057
X-RAY DIFFRACTIONf_plane_restr0.0041300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9599-2.02990.29014140.2637852X-RAY DIFFRACTION98
2.0299-2.11120.2764150.22937898X-RAY DIFFRACTION99
2.1112-2.20730.25654180.20137938X-RAY DIFFRACTION99
2.2073-2.32370.25964190.20227951X-RAY DIFFRACTION99
2.3237-2.46920.25954210.19858001X-RAY DIFFRACTION99
2.4692-2.65990.26574230.21378044X-RAY DIFFRACTION100
2.6599-2.92750.2564250.20668070X-RAY DIFFRACTION100
2.9275-3.3510.24064270.19168113X-RAY DIFFRACTION100
3.351-4.22160.18874300.16068171X-RAY DIFFRACTION100
4.2216-48.51760.19544440.16718457X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6258-0.46271.72320.47960.97855.5980.41110.3155-0.7606-0.1530.0820.16841.2301-0.1002-0.45180.440.0218-0.08040.2468-0.03330.3063-24.5638-84.430534.8401
21.6816-0.10651.98060.6534-0.17912.63620.25090.2188-0.1118-0.0412-0.0578-0.03310.39960.3357-0.15050.19190.0292-0.03620.2735-0.01810.1583-19.349-77.612638.5258
31.5484-0.99850.06891.42580.81732.8136-0.216-0.02730.5396-0.1213-0.0558-0.136-0.9631-0.92210.37530.50070.2926-0.10840.3626-0.07740.3433-33.0345-59.203340.6847
41.124-0.24821.39141.18670.57064.2778-0.4031-0.59240.3871-0.0633-0.03460.0511-0.7443-1.15790.45330.21550.1712-0.08170.3169-0.11110.1741-30.3061-63.481242.978
51.7334-0.02930.07310.96771.33691.8593-0.08570.0756-0.0707-0.077-0.0583-0.02410.0118-0.10260.10210.2335-0.0332-0.02830.16730.00160.215-41.2403-83.73164.6775
62.7169-0.64150.18291.12760.3570.18070.05050.7249-0.1741-0.2282-0.20170.095-0.03460.01350.14780.20170.0102-0.03850.2368-0.03780.1187-43.3999-86.5085-12.9974
72.5365-0.41660.08010.23410.19821.4017-0.0838-0.00050.5881-0.0439-0.0299-0.1657-0.27210.05710.11430.2238-0.0141-0.07160.1213-0.00150.3125-42.3315-70.36167.0092
83.08570.06661.2550.03370.11570.9798-0.4739-0.17660.4854-0.12060.2868-0.0947-0.5268-0.16580.25220.36360.0208-0.04530.1402-0.07060.3485-44.4607-67.04912.0028
91.71060.2769-2.03170.6497-0.00773.7010.3232-0.03290.29210.08370.02210.0551-0.5074-0.1262-0.25510.22970.00520.04290.2767-0.00030.1778-24.0881-121.13-35.8117
100.2107-0.1976-0.25680.3140.45430.8186-0.04960.1040.0143-0.15830.2595-0.20880.184-0.2019-0.11110.7177-0.48080.19460.6014-0.32690.7253-33.7704-145.6657-44.3914
111.807-0.1829-1.93330.62280.18313.9171-0.47551.0911-0.52910.00140.0380.21070.7419-1.66310.58780.1622-0.2980.07220.3125-0.22230.1255-30.7438-138.2548-43.5441
121.4533-0.0355-0.08870.86581.10091.7336-0.0769-0.00530.07280.1039-0.04120.02660.0275-0.10770.09240.20280.00820.0280.1423-0.01180.1857-42.5414-117.0617-5.1249
132.38690.5625-0.08890.96040.28690.14220.1021-0.58180.20910.27-0.25960.08860.0381-0.01130.09940.2357-0.04930.07240.2603-0.06140.2063-44.7479-113.651112.388
142.22680.4621-0.31430.41470.5081.5429-0.1523-0.0171-0.5660.14380.015-0.14440.38310.00010.14460.2094-0.00470.07140.0648-0.00090.2406-43.4273-130.6968-6.6997
15222222-12.89678.0246-0.7707-30.722513.45786.446210.535-2.3545-0.57061.04860.5131-0.13981.818-0.3580.7428-29.8364-141.9755-14.7176
162.92851.58130.33480.9508-0.23512.0123-0.17590.0052-0.4596-0.2080.0578-0.30550.4499-0.22680.06610.2631-0.05570.0970.175-0.03730.3001-46.9607-133.4139-10.8653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 19:67)
2X-RAY DIFFRACTION2(chain A and resid 68:116)
3X-RAY DIFFRACTION3(chain A and resid 117:153)
4X-RAY DIFFRACTION4(chain A and resid 154:238)
5X-RAY DIFFRACTION5(chain A and resid 239:301)
6X-RAY DIFFRACTION6(chain A and resid 302:332)
7X-RAY DIFFRACTION7(chain A and resid 333:449)
8X-RAY DIFFRACTION8(chain A and resid 450:469)
9X-RAY DIFFRACTION9(chain B and resid 19:127)
10X-RAY DIFFRACTION10(chain B and resid 128:150)
11X-RAY DIFFRACTION11(chain B and resid 151:238)
12X-RAY DIFFRACTION12(chain B and resid 239:301)
13X-RAY DIFFRACTION13(chain B and resid 302:332)
14X-RAY DIFFRACTION14(chain B and resid 333:450)
15X-RAY DIFFRACTION15(chain B and resid 457:457)
16X-RAY DIFFRACTION16(chain B and resid 458:469)

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