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- PDB-3bpp: 1510-N membrane protease K138A mutant specific for a stomatin hom... -

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Basic information

Entry
Database: PDB / ID: 3bpp
Title1510-N membrane protease K138A mutant specific for a stomatin homolog from Pyrococcus horikoshii
Components1510-N membrane protease
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYokoyama, H. / Hamamatsu, S. / Fujii, S. / Matsui, I.
Citation
Journal: J.SYNCHROTRON RADIAT. / Year: 2008
Title: Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin
Authors: Yokoyama, H. / Hamamatsu, S. / Fujii, S. / Matsui, I.
#1: 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.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1510-N membrane protease


Theoretical massNumber of molelcules
Total (without water)25,3681
Polymers25,3681
Non-polymers00
Water1,13563
1
A: 1510-N membrane protease

A: 1510-N membrane protease


Theoretical massNumber of molelcules
Total (without water)50,7362
Polymers50,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
2
A: 1510-N membrane protease

A: 1510-N membrane protease


Theoretical massNumber of molelcules
Total (without water)50,7362
Polymers50,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.261, 106.261, 128.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 25368.025 Da / Num. of mol.: 1 / Fragment: Residues 16-236 / Mutation: K138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / 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.: 63 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 18% PEG4000, 0.1M magnesium chloride, 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: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2006 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16792 / % possible obs: 99 % / Redundancy: 14.1 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 71.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 11.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DEO

2deo


Resolution: 2.3→19.51 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.011 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30976 1694 10.1 %RANDOM
Rwork0.23669 ---
obs0.24374 15063 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.985 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 0 63 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221693
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9742301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64524.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60915290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.271158
X-RAY DIFFRACTIONr_chiral_restr0.090.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021257
X-RAY DIFFRACTIONr_nbd_refined0.2210.2774
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.23
X-RAY DIFFRACTIONr_mcbond_it6.59621114
X-RAY DIFFRACTIONr_mcangle_it8.56231747
X-RAY DIFFRACTIONr_scbond_it6.4962669
X-RAY DIFFRACTIONr_scangle_it8.2023554
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 139 -
Rwork0.321 1070 -
obs--99.92 %

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