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- PDB-1wmi: Crystal structure of archaeal RelE-RelB complex from Pyrococcus h... -

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Basic information

Entry
Database: PDB / ID: 1wmi
TitleCrystal structure of archaeal RelE-RelB complex from Pyrococcus horikoshii OT3
Components
  • hypothetical protein PHS013Hypothesis
  • hypothetical protein PHS014Hypothesis
KeywordsHYDROLASE/HYDROLASE INHIBITOR / toxin-antitoxin complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Family of unknown function (DUF5646) / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Family of unknown function (DUF5646) / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsTakagi, H. / Kakuta, Y. / Kamachi, R. / Yao, M. / Tanaka, I. / Kimura, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects
Authors: Takagi, H. / Kakuta, Y. / Okada, T. / Yao, M. / Tanaka, I. / Kimura, M.
History
DepositionJul 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PHS013
B: hypothetical protein PHS014
C: hypothetical protein PHS013
D: hypothetical protein PHS014


Theoretical massNumber of molelcules
Total (without water)37,8164
Polymers37,8164
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein PHS013
B: hypothetical protein PHS014

A: hypothetical protein PHS013
B: hypothetical protein PHS014

C: hypothetical protein PHS013
D: hypothetical protein PHS014

C: hypothetical protein PHS013
D: hypothetical protein PHS014


Theoretical massNumber of molelcules
Total (without water)75,6318
Polymers75,6318
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_556-x,-y,z+11
Buried area22770 Å2
ΔGint-82 kcal/mol
Surface area27730 Å2
MethodPISA
3
A: hypothetical protein PHS013
B: hypothetical protein PHS014

C: hypothetical protein PHS013
D: hypothetical protein PHS014


Theoretical massNumber of molelcules
Total (without water)37,8164
Polymers37,8164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area10260 Å2
ΔGint-28 kcal/mol
Surface area14980 Å2
MethodPISA
4
A: hypothetical protein PHS013
B: hypothetical protein PHS014

C: hypothetical protein PHS013
D: hypothetical protein PHS014


Theoretical massNumber of molelcules
Total (without water)37,8164
Polymers37,8164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,-y,z+11
Buried area8720 Å2
ΔGint-30 kcal/mol
Surface area16530 Å2
MethodPISA
5
A: hypothetical protein PHS013
B: hypothetical protein PHS014


Theoretical massNumber of molelcules
Total (without water)18,9082
Polymers18,9082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
C: hypothetical protein PHS013
D: hypothetical protein PHS014


Theoretical massNumber of molelcules
Total (without water)18,9082
Polymers18,9082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.533, 142.651, 37.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hypothetical protein PHS013 / Hypothesis / RelE


Mass: 10904.917 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus (DE3)-RIL / References: UniProt: O73966
#2: Protein hypothetical protein PHS014 / Hypothesis / RelB


Mass: 8002.892 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus (DE3)-RIL / References: UniProt: O73967
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.7 Å3/Da / Density % sol: 23.5 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, hanging drop / pH: 7
Details: tri-Ammonium citrate, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9794, 0.9792, 0.9000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97921
30.91
ReflectionResolution: 2.3→50 Å / Num. all: 11170 / Num. obs: 11137 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.137 / % possible all: 72.3

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Processing

Software
NameClassification
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→10 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1071 10 %RANDOM
Rwork0.228 ---
all-11170 --
obs-11137 83.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 0 36 2544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.91

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