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- PDB-3wwv: C-terminal domain of stomatin operon partner protein 1510-C from ... -

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Basic information

Entry
Database: PDB / ID: 3wwv
TitleC-terminal domain of stomatin operon partner protein 1510-C from Pyrococcus horikoshii
ComponentsStomatin operon partner protein
KeywordsUNKNOWN FUNCTION / beta barrel / OB fold / membrane protein stomatin
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 domain / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...Archaeal protein PH0471, N-terminal / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Membrane-bound protease PH1510
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYokoyama, H. / Matsui, I.
Citation
Journal: FEBS Open Bio / Year: 2014
Title: Crystal structure of the stomatin operon partner protein from Pyrococcus horikoshii indicates the formation of a multimeric assembly
Authors: Yokoyama, H. / Matsui, I.
#1: Journal: Biochimie / Year: 2013
Title: Clustering of OB-fold domains of the partner protease complexed with trimeric stomatin from Thermococcales
Authors: Yokoyama, H. / Matsui, E. / Hiramoto, K. / Forterre, P. / Matsui, I.
History
DepositionJun 30, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stomatin operon partner protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2092
Polymers9,1861
Non-polymers231
Water36020
1
A: Stomatin operon partner protein
hetero molecules

A: Stomatin operon partner protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4174
Polymers18,3712
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area1400 Å2
ΔGint-5 kcal/mol
Surface area7160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.847, 75.847, 43.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-501-

NA

21A-620-

HOH

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Components

#1: Protein Stomatin operon partner protein / NfeD homolog / Membrane-bound protease PH1510 / STOPP


Mass: 9185.729 Da / Num. of mol.: 1 / Fragment: C-terminal domain, Residues 371-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: PH1510 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlusRIL / References: UniProt: O59179
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% Jeffamine M-600, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2013 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→19.57 Å / Num. obs: 3165 / % possible obs: 99.7 % / Redundancy: 10 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 6.9 / Num. unique all: 443 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
REFMAC5.8.0048refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EXD

2exd


Resolution: 2.4→18.96 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.997 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25796 288 9.1 %RANDOM
Rwork0.22084 ---
obs0.22464 2865 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.797 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→18.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms507 0 1 20 528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.999677
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.808563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74823.33321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51815115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.193156
X-RAY DIFFRACTIONr_chiral_restr0.0760.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6492.955255
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8954.411317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2093.302255
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.38524.056726
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 19 -
Rwork0.222 208 -
obs--100 %

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