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- PDB-2yys: Crystal structure of the proline iminopeptidase-related protein T... -

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Basic information

Entry
Database: PDB / ID: 2yys
TitleCrystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8
ComponentsProline iminopeptidase-related protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TTHA1809 / proline iminopeptidase-related protein
Function / homology
Function and homology information


peptidase activity / proteolysis / membrane
Similarity search - Function
Peptidase S33 / : / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Proline iminopeptidase-related protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsOkai, M. / Miyauchi, Y. / Ebihara, A. / Lee, W.C. / Nagata, K. / Tanokura, M.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8
Authors: Okai, M. / Miyauchi, Y. / Ebihara, A. / Lee, W.C. / Nagata, K. / Tanokura, M.
History
DepositionMay 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Proline iminopeptidase-related protein
B: Proline iminopeptidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7138
Polymers63,1602
Non-polymers5536
Water7,440413
1
A: Proline iminopeptidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8564
Polymers31,5801
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proline iminopeptidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8564
Polymers31,5801
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.930, 126.930, 114.295
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Proline iminopeptidase-related protein


Mass: 31579.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHC1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 4.2 Å3/Da / Density % sol: 70.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100mM HEPES-Na, 0.85M potassium sodium tartrate tetrahydrate, pH 7.2, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 51211

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.665 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20835 2740 5.1 %RANDOM
Rwork0.17655 ---
obs0.17812 51211 99.68 %-
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: 25.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.49 Å20 Å2
2--0.99 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 36 413 4856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214562
X-RAY DIFFRACTIONr_bond_other_d0.0050.024277
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9936213
X-RAY DIFFRACTIONr_angle_other_deg0.75339865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345562
X-RAY DIFFRACTIONr_chiral_restr0.0680.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025126
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02981
X-RAY DIFFRACTIONr_nbd_refined0.2060.2876
X-RAY DIFFRACTIONr_nbd_other0.2470.24623
X-RAY DIFFRACTIONr_nbtor_other0.0820.22424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2316
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.213
X-RAY DIFFRACTIONr_mcbond_it0.6861.52812
X-RAY DIFFRACTIONr_mcangle_it1.32524479
X-RAY DIFFRACTIONr_scbond_it1.7631750
X-RAY DIFFRACTIONr_scangle_it3.1544.51734
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 223
Rwork0.205 3686

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