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- PDB-3zvk: Crystal structure of VapBC2 from Rickettsia felis bound to a DNA ... -

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Basic information

Entry
Database: PDB / ID: 3zvk
TitleCrystal structure of VapBC2 from Rickettsia felis bound to a DNA fragment from their promoter
Components
  • (DNA) x 2
  • ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB
  • TOXIN OF TOXIN-ANTITOXIN SYSTEM
KeywordsANTITOXIN/TOXIN/DNA / ANTITOXIN-TOXIN-DNA COMPLEX / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily ...Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Ribonuclease VapC2 / Antitoxin VapB2
Similarity search - Component
Biological speciesRICKETTSIA FELIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsMate, M.J. / Ortiz-Lombardia, M. / Cambillau, C.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal Structure of the DNA-Bound Vapbc2 Antitoxin/Toxin Pair from Rickettsia Felis.
Authors: Mate, M.J. / Vincentelli, R. / Foos, N. / Raoult, D. / Cambillau, C. / Ortiz-Lombardia, M.
History
DepositionJul 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Apr 25, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOXIN OF TOXIN-ANTITOXIN SYSTEM
B: TOXIN OF TOXIN-ANTITOXIN SYSTEM
C: TOXIN OF TOXIN-ANTITOXIN SYSTEM
D: TOXIN OF TOXIN-ANTITOXIN SYSTEM
E: ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB
F: ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB
G: ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB
H: ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB
X: DNA
Y: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,11414
Polymers113,33310
Non-polymers7814
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33740 Å2
ΔGint-151.7 kcal/mol
Surface area38650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.780, 92.333, 150.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
TOXIN OF TOXIN-ANTITOXIN SYSTEM / VAPC2


Mass: 15318.621 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RICKETTSIA FELIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4UNB2
#2: Protein
ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB / VAPB2


Mass: 9023.481 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RICKETTSIA FELIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4UNB3

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DNA chain , 2 types, 2 molecules XY

#3: DNA chain DNA


Mass: 8022.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: VAPBC2 PROMOTOR FRAGMENT / Source: (synth.) RICKETTSIA FELIS (bacteria)
#4: DNA chain DNA


Mass: 7942.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: VAPBC2 PROMOTOR FRAGMENT / Source: (synth.) RICKETTSIA FELIS (bacteria)

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Non-polymers , 2 types, 360 molecules

#5: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 6 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 6 TO GLY ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, ASP 6 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 6 TO GLY ENGINEERED RESIDUE IN CHAIN C, ASP 6 TO GLY ENGINEERED RESIDUE IN CHAIN D, ASP 6 TO GLY

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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: 2.4 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growpH: 6.5 / Details: 12% PEG4000, 4% PEG400, 100MM MES PH6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID23-110.9334
SYNCHROTRONESRF ID14-420.9334
Detector
TypeIDDetectorDate
ADSC CCD1CCDFeb 26, 2009
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.93341
20.93341
ReflectionResolution: 2.5→47.29 Å / Num. obs: 39577 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 63.43 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.4
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.9.5refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.5→36.42 Å / Cor.coef. Fo:Fc: 0.9452 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.444 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.508 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1983 5.02 %RANDOM
Rwork0.1723 ---
obs0.1745 39514 99.6 %-
Displacement parametersBiso mean: 67.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.894 Å20 Å20 Å2
2--8.9259 Å20 Å2
3----12.8199 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 1063 48 356 7725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017890HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2810863HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3172SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes192HARMONIC2
X-RAY DIFFRACTIONt_gen_planes952HARMONIC5
X-RAY DIFFRACTIONt_it7890HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion21.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1028SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8702SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2447 135 4.66 %
Rwork0.2059 2761 -
all0.2077 2896 -
obs--99.6 %
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)
12.1652-0.09740.95042.672-0.60341.0071-0.035-0.3628-0.12690.36610.0710.4887-0.0454-0.1544-0.036-0.17120.00670.0814-0.12790.00560.1677-6.4547-13.1172-30.5356
22.91030.52311.38772.4362-1.10423.75930.1181-0.2401-0.5140.5357-0.2187-0.44060.120.33170.1006-0.10740.0335-0.0419-0.18220.11280.139213.7874-24.3416-21.1678
32.8508-0.8396-2.28192.25370.79593.59240.1709-0.5680.07190.17530.1075-0.2741-0.27440.2908-0.2784-0.1797-0.0475-0.0557-0.0476-0.00970.033449.325214.1867-19.6001
42.5585-0.5248-0.92642.85021.50443.8863-0.1988-0.0092-0.86850.2934-0.030.38110.6939-0.36030.2288-0.2349-0.06230.0368-0.2424-0.01110.271144.9532-8.3782-30.0395
53.83071.7233-0.34973.90690.31120.8898-0.07350.47770.0941-0.54950.14980.0678-0.14750.0274-0.0763-0.02790.0133-0.0181-0.04850.0067-0.05167.9193-2.6453-48
62.21161.11361.04211.97060.83841.31320.1253-0.4421-0.37010.3218-0.0949-0.05210.2294-0.1151-0.0304-0.04320.00250.0810.01820.1494-0.176117.4754-9.4554-11.0451
72.7416-0.0169-1.30510.15630.16532.33870.0231-0.7653-0.37730.2307-0.0134-0.15770.06480.2097-0.0098-0.04370.0075-0.03560.04790.0595-0.120138.0497.4934-9.1228
83.65621.29250.64071.49121.25850.45330.0650.2477-0.6031-0.27530.1074-0.2776-0.25420.1321-0.1724-0.0619-0.03030.0425-0.0789-0.07250.085421.2198-4.7255-46.2555
92.64840.42420.53161.83770.34847.3479-0.0131-0.010.0904-0.31920.3116-0.136-0.2901-0.327-0.2985-0.2428-0.0150.0272-0.2411-0.0108-0.232217.76539.5866-29.9591
103.60620.06480.65882.33980.87473.9422-0.0264-0.40910.04920.06380.2996-0.1735-0.1359-0.2437-0.2732-0.2572-0.00780.0195-0.2515-0.0518-0.270816.94489.9564-30.1238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)
3X-RAY DIFFRACTION3(CHAIN C)
4X-RAY DIFFRACTION4(CHAIN D)
5X-RAY DIFFRACTION5(CHAIN E)
6X-RAY DIFFRACTION6(CHAIN F)
7X-RAY DIFFRACTION7(CHAIN G)
8X-RAY DIFFRACTION8(CHAIN H)
9X-RAY DIFFRACTION9(CHAIN X AND RESID 2:27)
10X-RAY DIFFRACTION10(CHAIN Y AND RESID 1:26)

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