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- PDB-2deo: 1510-N membrane protease specific for a stomatin homolog from Pyr... -

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Basic information

Entry
Database: PDB / ID: 2deo
Title1510-N membrane protease specific for a stomatin homolog from Pyrococcus horikoshii
Components441aa long hypothetical nfeD protein
KeywordsHYDROLASE / membrane protease / specific for a stomatin homolog / archaea / Pyrococcus / thermostable / catalytic dyad
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / membrane
Similarity search - Function
Archaeal protein PH0471, N-terminal / NfeD-like, C-terminal domain / NfeD-like C-terminal, partner-binding / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Membrane-bound protease PH1510
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsYokoyama, H. / Matsui, I.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Molecular Structure of a Novel Membrane Protease Specific for a Stomatin Homolog from the Hyperthermophilic Archaeon Pyrococcus horikoshii
Authors: Yokoyama, H. / Matsui, E. / Akiba, T. / Harata, K. / Matsui, I.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: A novel thermostable membrane protease forming an operon with a stomatin homolog from the hyperthermophilic archaebacterium Pyrococcus horikoshii
Authors: Yokoyama, H. / Matsui, I.
History
DepositionFeb 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 441aa long hypothetical nfeD protein
B: 441aa long hypothetical nfeD protein


Theoretical massNumber of molelcules
Total (without water)51,3212
Polymers51,3212
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.212, 108.400, 59.342
Angle α, β, γ (deg.)90.00, 110.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 441aa long hypothetical nfeD protein / 1510-N membrane protease


Mass: 25660.604 Da / Num. of mol.: 2 / Fragment: Residues 16-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1510 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: O59179
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 21% PEG8000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9789, 0.9792, 0.9900
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Dec 19, 2004 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97921
30.991
ReflectionResolution: 3→20 Å / Num. obs: 12407 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 25.2
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3→19.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2211094.98 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1263 10.3 %RANDOM
Rwork0.198 ---
obs0.198 12305 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70 Å2 / ksol: 0.244179 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 3→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 0 32 3124
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.63
X-RAY DIFFRACTIONc_mcbond_it4.831.5
X-RAY DIFFRACTIONc_mcangle_it7.332
X-RAY DIFFRACTIONc_scbond_it6.532
X-RAY DIFFRACTIONc_scangle_it11.112.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 217 10.7 %
Rwork0.258 1803 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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