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- PDB-2p5t: Molecular and structural characterization of the PezAT chromosoma... -

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Basic information

Entry
Database: PDB / ID: 2p5t
TitleMolecular and structural characterization of the PezAT chromosomal toxin-antitoxin system of the human pathogen Streptococcus pneumoniae
Components
  • PezT
  • Putative transcriptional regulator PezA
  • fragment of PezA helix-turn-helix motif
KeywordsTRANSCRIPTION REGULATOR / postsegregational killing system / phosphoryltransferase / helix-turn-helix motif
Function / homology
Function and homology information


UDP-N-acetylglucosamine kinase / : / kinase activity / DNA binding / ATP binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #130 / Antitoxin epsilon/PezA domain superfamily / Zeta toxin domain / Zeta toxin / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Helicase, Ruva Protein; domain 3 ...Helicase, Ruva Protein; domain 3 - #130 / Antitoxin epsilon/PezA domain superfamily / Zeta toxin domain / Zeta toxin / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Toxin PezT / Antitoxin PezA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsLoll, B. / Meinhart, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Molecular and Structural Characterization of the PezAT Chromosomal Toxin-Antitoxin System of the Human Pathogen Streptococcus pneumoniae.
Authors: Khoo, S.K. / Loll, B. / Chan, W.T. / Shoeman, R.L. / Ngoo, L. / Yeo, C.C. / Meinhart, A.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE CHAIN X IS THE N-TERMINAL DOMAIN OF EITHER CHAIN A,C,E OR G. BECAUSE THE ELECTRON DENSITY ...SEQUENCE CHAIN X IS THE N-TERMINAL DOMAIN OF EITHER CHAIN A,C,E OR G. BECAUSE THE ELECTRON DENSITY FOR THE FIRST 33 AMINO ACIDS OF CHAIN X WAS POOR, THE AUTHORS WERE UNABLE TO ASSIGN SIDE CHAINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: fragment of PezA helix-turn-helix motif
A: Putative transcriptional regulator PezA
B: PezT
C: Putative transcriptional regulator PezA
D: PezT
E: Putative transcriptional regulator PezA
F: PezT
G: Putative transcriptional regulator PezA
H: PezT


Theoretical massNumber of molelcules
Total (without water)192,3229
Polymers192,3229
Non-polymers00
Water0
1
A: Putative transcriptional regulator PezA
B: PezT
C: Putative transcriptional regulator PezA
D: PezT


Theoretical massNumber of molelcules
Total (without water)94,7484
Polymers94,7484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-25 kcal/mol
Surface area32510 Å2
MethodPISA
2
X: fragment of PezA helix-turn-helix motif
E: Putative transcriptional regulator PezA
F: PezT
G: Putative transcriptional regulator PezA
H: PezT


Theoretical massNumber of molelcules
Total (without water)97,5745
Polymers97,5745
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Putative transcriptional regulator PezA
F: PezT
G: Putative transcriptional regulator PezA
H: PezT


Theoretical massNumber of molelcules
Total (without water)94,7484
Polymers94,7484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-33 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.520, 102.860, 254.440
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/peptide fragment of PezA helix-turn-helix motif


Mass: 2826.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Codon Plus-RIL
#2: Protein
Putative transcriptional regulator PezA


Mass: 18267.666 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Codon Plus-RIL / References: UniProt: Q97QZ2
#3: Protein
PezT


Mass: 29106.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Codon Plus-RIL / References: UniProt: Q97QZ1

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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: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12.5-15% (v/v) iso-propanol, 100 mM MES-NaOH, 6% (v/v) dioxane (30% (v/v)), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.007466
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007466 Å / Relative weight: 1
ReflectionResolution: 3.2→47.67 Å / Num. all: 34352 / Num. obs: 34352 / % possible obs: 95.3 % / Observed criterion σ(F): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 76.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.8
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4708 / % possible all: 85.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→47.67 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 55.632 / SU ML: 0.426 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27732 1726 4.9 %RANDOM
Rwork0.21368 ---
obs0.21692 33459 100 %-
all-34352 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11093 0 0 0 11093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211256
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.97915145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15151366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72324.892556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17152160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8361572
X-RAY DIFFRACTIONr_chiral_restr0.070.21686
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028380
X-RAY DIFFRACTIONr_nbd_refined0.2060.25231
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2356
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.26
X-RAY DIFFRACTIONr_mcbond_it0.3581.56996
X-RAY DIFFRACTIONr_mcangle_it0.648210967
X-RAY DIFFRACTIONr_scbond_it0.66834751
X-RAY DIFFRACTIONr_scangle_it1.1644.54178
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 115 -
Rwork0.277 2270 -
obs-2385 100 %
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)
14.0021-1.81762.82151.9505-1.76623.2893-0.1635-0.67950.0220.29630.19370.2032-0.4191-0.4528-0.0302-0.04590.14750.09830.07780.0231-0.079643.9918-5.785349.551
25.48960.4047-2.10461.5392-0.77511.9120.06250.31160.2891-0.33790.0250.0040.0233-0.1501-0.0875-0.0823-0.006-0.085-0.44340.0565-0.126345.035411.21128.406
30.8553-0.48480.23485.8459-1.97782.8569-0.0240.13340.1744-0.3619-0.0537-0.1137-0.0926-0.17240.0777-0.2961-0.0449-0.0847-0.0577-0.0335-0.339245.5727-13.7078-56.154
42.0961.27521.69672.76141.31973.137-0.17330.04350.34670.08940.01130.2105-0.2046-0.09240.162-0.35070.00410.0696-0.26030.1376-0.399564.2318-17.6567-16.8755
55.45715.328111.123143.015627.378429.8877-0.9131-0.5106-0.06090.9301-0.2331-0.24360.16160.18171.14620.18520.19360.29490.37150.2870.254959.5314-23.72410.6405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB67 - 15867 - 158
2X-RAY DIFFRACTION1BC3 - 1683 - 168
3X-RAY DIFFRACTION1BC176 - 253176 - 253
4X-RAY DIFFRACTION2CD66 - 15866 - 158
5X-RAY DIFFRACTION2DE1 - 1681 - 168
6X-RAY DIFFRACTION2DE173 - 251173 - 251
7X-RAY DIFFRACTION3EF64 - 15864 - 158
8X-RAY DIFFRACTION3FG2 - 1652 - 165
9X-RAY DIFFRACTION3FG178 - 253178 - 253
10X-RAY DIFFRACTION4GH66 - 15866 - 158
11X-RAY DIFFRACTION4HI1 - 1661 - 166
12X-RAY DIFFRACTION4HI178 - 253178 - 253
13X-RAY DIFFRACTION5XA1 - 331 - 33

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