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- PDB-3eoq: The crystal structure of putative zinc protease beta-subunit from... -

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Basic information

Entry
Database: PDB / ID: 3eoq
TitleThe crystal structure of putative zinc protease beta-subunit from Thermus thermophilus HB8
ComponentsPutative zinc protease
KeywordsHYDROLASE / two similar domains of beta(2)-alpha(2)-beta(2)-alpha(5)-beta structure / Protease
Function / homology
Function and homology information


peptidase activity / proteolysis / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / : / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsOhtsuka, J. / Ichihara, Y. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Nagata, K. / Tanokura, M.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase.
Authors: Ohtsuka, J. / Ichihara, Y. / Ebihara, A. / Nagata, K. / Tanokura, M.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative zinc protease
B: Putative zinc protease


Theoretical massNumber of molelcules
Total (without water)92,1182
Polymers92,1182
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.340, 94.202, 134.454
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 Putative zinc protease


Mass: 46058.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1264 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIV0, insulysin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15M DL-MALIC ACID, 22% PEG 3350, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 61353 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.7 Å2
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.29→48.62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.367 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2015 5 %RANDOM
Rwork0.187 ---
obs0.19 38618 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.29→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6435 0 0 304 6739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226577
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9738889
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16622.5336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4591574
X-RAY DIFFRACTIONr_chiral_restr0.0880.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025142
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22962
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24466
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2369
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.54170
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16126377
X-RAY DIFFRACTIONr_scbond_it1.96632752
X-RAY DIFFRACTIONr_scangle_it3.0074.52512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 139 -
Rwork0.191 2690 -
obs--94.55 %

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