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- PDB-1yr2: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases:... -

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Basic information

Entry
Database: PDB / ID: 1yr2
TitleStructural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain Dynamics in Catalysis and Specificity
Componentsprolyl oligopeptidaseProlyl endopeptidase
KeywordsHYDROLASE / prolyl endopeptidase / mechanistic study / celiac sprue
Function / homology
Function and homology information


prolyl oligopeptidase / serine-type endopeptidase activity
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Prolyl oligopeptidase
Similarity search - Component
Biological speciesNovosphingobium capsulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsShan, L. / Mathews, I.I. / Khosla, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Interdomain Dynamics in Catalysis and Specificity
Authors: Shan, L. / Mathews, I.I. / Khosla, C.
#1: Journal: Biochem.J. / Year: 2004
Title: Comparative biochemical analysis of three bacterial prolyl endopeptidases: implications for celiac sprue
Authors: Shan, L. / Marti, T. / Sollid, L.M. / Gray, G.M. / Khosla, C.
#2: Journal: Science / Year: 2002
Title: Structural basis for gluten intolerance in Celiac Sprue
Authors: Shan, L. / Molberg, O. / Parroit, I. / Hausch, F. / Filiz, F. / Gray, G.M. / Sollid, L.M. / Khosla, C.
#3: Journal: CELL.MOL.LIFE SCI. / Year: 2002
Title: The prolyl oligopeptidase family
Authors: Polgar, L.
History
DepositionFeb 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The conflict may be due to a different lab strain.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prolyl oligopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8423
Polymers80,6581
Non-polymers1842
Water11,890660
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.341, 91.224, 79.787
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein prolyl oligopeptidase / Prolyl endopeptidase / prolyl endopeptidases


Mass: 80657.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium capsulatum (bacteria) / Gene: ATCC / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9ZNM8, prolyl oligopeptidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG 8000, Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 11, 2003 / Details: monochromator
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 68648 / Num. obs: 68648 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.071 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 6381 / Rsym value: 0.502 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1H2W

1h2w


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.545 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18614 3538 5.1 %RANDOM
Rwork0.161 ---
all0.1622 66171 --
obs0.16229 66171 98.56 %-
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: 15.553 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-0.13 Å2
2--1.93 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5251 0 12 660 5923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215419
X-RAY DIFFRACTIONr_bond_other_d0.0020.024839
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9397388
X-RAY DIFFRACTIONr_angle_other_deg1.026311222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815676
X-RAY DIFFRACTIONr_chiral_restr0.1010.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026119
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021155
X-RAY DIFFRACTIONr_nbd_refined0.2010.2890
X-RAY DIFFRACTIONr_nbd_other0.2620.25346
X-RAY DIFFRACTIONr_nbtor_other0.0870.23121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2481
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.212
X-RAY DIFFRACTIONr_mcbond_it0.9881.53382
X-RAY DIFFRACTIONr_mcangle_it1.75525418
X-RAY DIFFRACTIONr_scbond_it2.76432037
X-RAY DIFFRACTIONr_scangle_it4.3524.51970
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.263 237
Rwork0.25 4393
obs-4630
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84830.06240.46360.33010.24630.93850.05160.08560.0228-0.0592-0.0105-0.03840.05450.0358-0.04110.0780.0360.02420.04140.02230.026742.098640.9254-30.0682
230.01914.4798-8.22040.3293-3.5085.02650.1958-0.8422-0.3150.1928-0.1848-0.1090.24820.1362-0.0110.0768-0.0013-0.04860.0666-0.00130.074679.641444.0146-14.2893
31.0595-0.0512-0.18060.3179-0.13310.76440.0194-0.0941-0.01910.0122-0.0204-0.0287-0.0196-0.02770.0010.0384-0.0041-0.01740.0175-0.0170.053837.969249.82868.853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA38 - 10738 - 107
2X-RAY DIFFRACTION1AA453 - 725453 - 725
3X-RAY DIFFRACTION2AA726 - 738726 - 738
4X-RAY DIFFRACTION3AA108 - 452108 - 452

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