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- PDB-1x2b: The crystal structure of prolyl aminopeptidase complexed with Sar... -

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Basic information

Entry
Database: PDB / ID: 1x2b
TitleThe crystal structure of prolyl aminopeptidase complexed with Sar-TBODA
ComponentsProline iminopeptidase
KeywordsHYDROLASE / prolyl aminopeptidase / binary complex / prolyl iminopeptidase / alpha/beta-hydrolase
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
Chem-STX / Proline iminopeptidase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsNakajima, Y. / Ito, K. / Sakata, M. / Xu, Y. / Matsubara, F. / Hatakeyama, S. / Yoshimoto, T.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens
Authors: Nakajima, Y. / Ito, K. / Sakata, M. / Xu, Y. / Nakashima, K. / Matsubara, F. / Hatakeyama, S. / Yoshimoto, T.
History
DepositionApr 22, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3282
Polymers36,1311
Non-polymers1971
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.241, 65.241, 169.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is the monomer in asymmetric unit.

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Components

#1: Protein Proline iminopeptidase / PIP / Prolyl aminopeptidase / PAP


Mass: 36130.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: O32449, prolyl aminopeptidase
#2: Chemical ChemComp-STX / 1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-2-(METHYLAMINO)ETHANONE / 2-SARCOSINYL-5-TERT-BUTYL-[1,3,4]-OXADIAZOLE


Mass: 197.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, cacodylate, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2003
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 14640 / Num. obs: 14640 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.059 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 2107 / Rsym value: 0.222 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1QTR

1qtr


Resolution: 2.4→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 740 -random
Rwork0.191 ---
all-14599 --
obs-14599 97.3 %-
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.063 Å20 Å20 Å2
2---4.063 Å20 Å2
3---8.126 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 14 43 2571
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.198
X-RAY DIFFRACTIONc_dihedral_angle_d22.63
X-RAY DIFFRACTIONc_improper_angle_d0.727
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.272 79 -
Rwork0.239 --
obs-1448 99.5 %

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