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- PDB-4gf1: Crystal Structure of Certhrax -

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Basic information

Entry
Database: PDB / ID: 4gf1
TitleCrystal Structure of Certhrax
ComponentsPutative ADP-ribosyltransferase Certhrax
KeywordsTRANSFERASE / ADP-ribosyltransferase
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
Putative ADP-ribosyltransferase Certhrax
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsHong, B.S. / Dimov, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Park, H. / Structural Genomics Consortium (SGC)
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
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,1488
Polymers107,1482
Non-polymers06
Water1,04558
1
A: Putative ADP-ribosyltransferase Certhrax


Theoretical massNumber of molelcules
Total (without water)53,5746
Polymers53,5741
Non-polymers05
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ADP-ribosyltransferase Certhrax


Theoretical massNumber of molelcules
Total (without water)53,5742
Polymers53,5741
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.725, 95.966, 190.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / Gene: BCE_G9241_pBC218_0027 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4MV79, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.8 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.2
Details: 5 micromoles of suramin and 1:100 mol/mol of elastase were added to protein stock solution. Crystallization condition: 2.4M sodium malonate, 0.01M HEPES, pH 7.2, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.206→95.42 Å / Num. all: 53961 / Num. obs: 53961 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rsym value: 0.093 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.377.70.9240.85947677740.92498.3
2.37-2.527.60.5671.35545672670.56798.4
2.52-2.697.60.37225271269210.37298.6
2.69-2.97.60.2343.24891064660.23498.9
2.9-3.187.50.1385.44473759780.13899
3.18-3.567.20.08883944354650.08899.3
3.56-4.116.90.06510.13342548320.06599.4
4.11-5.036.70.05611.42790641370.05699.6
5.03-7.126.80.04912.52231732640.04999.7
7.12-47.9836.30.04311.11163618570.04397.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4fk7

4fk7


Resolution: 2.25→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.216 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.113 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. coot and the molprobity server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 1486 2.756 %THIN SHELLS (SFTOOLS)
Rwork0.2211 ---
obs0.222 53925 98.448 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 138.25 Å2 / Biso mean: 56.268 Å2 / Biso min: 2.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.841 Å20 Å20 Å2
2--4.524 Å20 Å2
3----2.683 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6734 0 6 58 6798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026882
X-RAY DIFFRACTIONr_bond_other_d0.0050.026170
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9519331
X-RAY DIFFRACTIONr_angle_other_deg0.982314127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42324.921317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7661520
X-RAY DIFFRACTIONr_chiral_restr0.0770.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027938
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.3080.3021390.3093754397298.011
2.308-2.3710.2941210.2793724392897.887
2.371-2.440.313180.2723635372997.962
2.44-2.5150.321240.2733478366698.254
2.515-2.5970.3021170.2753398357398.377
2.597-2.6870.331150.2463266344098.285
2.687-2.7880.249960.253189333398.56
2.788-2.9020.269750.2483086320398.689
2.902-3.030.309990.2352942308598.574
3.03-3.1770.282660.2342856295698.85
3.177-3.3480.272740.2212718282598.832
3.348-3.5490.265680.2122584267599.14
3.549-3.7920.214430.1962458252998.893
3.792-4.0930.192960.1822246236599.027
4.093-4.4790.191400.1762115217499.126
4.479-50.22720.1691897198199.394
5-5.7580.185250.2091747178299.439
5.758-7.0160.249490.2381462151999.473
7.016-9.7730.272240.2151184121899.179
9.773-400.284250.28969375894.723
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)
17.1056-0.4964-3.372.791-0.50016.55140.41220.56360.9838-0.0327-0.0118-0.0178-0.8811-0.2827-0.40040.19340.06320.03350.17820.09570.1599-6.8684-17.932237.4383
26.21750.8302-2.933.276-1.26896.3229-0.5972-0.1484-1.181-0.1427-0.0028-0.05051.2910.50940.60.28190.11220.1070.16450.0520.2619-2.3626-37.195743.1841
312.50233.3418-13.67521.1137-4.22121.53940.0134-0.8305-0.1011-0.067-0.3304-0.3024-0.29481.76080.3170.1099-0.00990.0860.59150.1310.444614.8667-24.551136.0681
43.37-0.24020.29762.0313-3.1275.28220.10420.4435-0.188-0.05660.00230.1770.0702-0.2183-0.10640.25820.0250.03890.23750.02820.252210.9202-14.25680.1697
52.51640.9475-1.26274.6217-2.50934.849-0.01170.0873-0.6837-0.2021-0.14170.05550.6922-0.10110.15340.34910.05540.03220.18190.02410.4110.4645-29.04569.9753
67.24880.9138-3.5362.33870.626.86740.3960.05840.9160.078-0.0343-0.0435-0.7708-0.4187-0.36180.09760.05720.02780.3170.01140.1334-24.4703-18.920159.3924
77.7376-0.7913-3.16592.96091.64936.6509-0.68421.1605-1.3990.0728-0.0328-0.1351.3622-1.44090.7170.3258-0.31530.16040.6936-0.2550.3337-29.5491-37.069251.4181
811.8845-2.8832-14.67140.9213.336225.830.10610.54790.3631-0.00130.00250.2072-0.1307-1.0232-0.10860.01850.01130.03270.84940.02840.4845-46.3255-25.796159.7787
93.10990.3080.04151.51760.79493.98830.0296-0.3018-0.00540.0741-0.08290.0779-0.16330.06830.05330.0940.01840.00860.1569-0.02160.0676-43.5714-15.237796.4053
103.88741.2772-0.10992.0520.5173.4715-0.01420.0639-0.7885-0.00350.0324-0.2010.52810.2707-0.01820.16630.0657-0.0050.1561-0.0250.2132-44.0111-30.218688.0442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 123
2X-RAY DIFFRACTION2A124 - 224
3X-RAY DIFFRACTION3A225 - 242
4X-RAY DIFFRACTION4A243 - 330
5X-RAY DIFFRACTION5A331 - 480
6X-RAY DIFFRACTION6B1 - 123
7X-RAY DIFFRACTION7B124 - 224
8X-RAY DIFFRACTION8B225 - 242
9X-RAY DIFFRACTION9B243 - 330
10X-RAY DIFFRACTION10B331 - 480

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