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- PDB-1qtr: CRYSTAL STRUCTURE ANALYSIS OF THE PROLYL AMINOPEPTIDASE FROM SERR... -

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Basic information

Entry
Database: PDB / ID: 1qtr
TitleCRYSTAL STRUCTURE ANALYSIS OF THE PROLYL AMINOPEPTIDASE FROM SERRATIA MARCESCENS
ComponentsPROLYL AMINOPEPTIDASE
KeywordsHYDROLASE / ALPHA BETA HYDROLASE FOLD / PROLINE / PROLYL AMINOPEPTIDASE / SERRATIA / IMINOPEPTIDASE
Function / homology
Function and homology information


prolyl aminopeptidase / aminopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Proline iminopeptidase / Peptidase S33 / alpha/beta hydrolase fold / 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
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.32 Å
AuthorsYoshimoto, T. / Kabashima, T. / Uchikawa, K. / Inoue, T. / Tanaka, N.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1999
Title: Crystal structure of prolyl aminopeptidase from Serratia marcescens.
Authors: Yoshimoto, T. / Kabashima, T. / Uchikawa, K. / Inoue, T. / Tanaka, N. / Nakamura, K.T. / Tsuru, M. / Ito, K.
#1: Journal: J.Biochem.(Tokyo) / Year: 1997
Title: Prolyl Aminopeptidase from Serratia marcescens : Sequencing and Expression
Authors: Kabashima, T. / Kitazono, A. / Kitano, A. / Inoue, K. / Yoshimoto, T.
#2: Journal: J.Biochem.(Tokyo) / Year: 1994
Title: Prolyl aminopeptidase is not a sulfhydryl enzyme: Identification of the active serine residue by site-directed mutagenesis
Authors: Kitazono, A. / Ito, K. / Yoshimoto, T.
History
DepositionJun 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLYL AMINOPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)36,1311
Polymers36,1311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.36, 65.36, 169.2
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROLYL AMINOPEPTIDASE


Mass: 36130.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: PSPAP-HE / Production host: Escherichia coli (E. coli) / References: UniProt: O32449, prolyl aminopeptidase

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, SODIUM ACETATE, NA CACODYLATE/KH2PO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Kabashima, T., (1997) J.Biochem.(Tokyo), 122, 601.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 mg/mlprotein1drop
20.1 MNa-cacodylate1reservoir
30.2 MNa acetate1reservoir
420 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→10 Å / Num. obs: 45646 / % possible obs: 89.1 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Num. obs: 14917 / Num. measured all: 45646

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Processing

Software
NameClassification
DMmodel building
X-PLORrefinement
DMphasing
RefinementResolution: 2.32→8 Å / σ(F): 1
RfactorNum. reflectionSelection details
Rfree0.267 -RANDOM
Rwork0.189 --
obs0.189 45646 -
Refinement stepCycle: LAST / Resolution: 2.32→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 0 0 2530
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.39

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