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- PDB-1azw: PROLINE IMINOPEPTIDASE FROM XANTHOMONAS CAMPESTRIS PV. CITRI -

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Basic information

Entry
Database: PDB / ID: 1azw
TitlePROLINE IMINOPEPTIDASE FROM XANTHOMONAS CAMPESTRIS PV. CITRI
ComponentsPROLINE IMINOPEPTIDASE
KeywordsAMINOPEPTIDASE / PROLINE IMINOPEPTIDASE / SERINE PROTEASE / XANTHOMONAS CAMPESTRIS
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 speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.7 Å
AuthorsMedrano, F.J. / Alonso, J. / Garcia, J.L. / Romero, A. / Bode, W. / Gomis-Ruth, F.X.
Citation
Journal: EMBO J. / Year: 1998
Title: Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family.
Authors: Medrano, F.J. / Alonso, J. / Garcia, J.L. / Romero, A. / Bode, W. / Gomis-Ruth, F.X.
#1: Journal: FEBS Lett. / Year: 1997
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Proline Iminopeptidase from Xanthomonas Campestris Pv. Citri
Authors: Medrano, F.J. / Alonso, J. / Garcia, J.L. / Bode, W. / Gomis-Ruth, F.X.
History
DepositionNov 22, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLINE IMINOPEPTIDASE
B: PROLINE IMINOPEPTIDASE


Theoretical massNumber of molelcules
Total (without water)71,0412
Polymers71,0412
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.200, 167.800, 85.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.735159, -0.677868, -0.006), (-0.677881, 0.735171, 0.00029), (0.004214, 0.004281, -0.999982)
Vector: 92.4586, 36.07255, 114.15431)

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Components

#1: Protein PROLINE IMINOPEPTIDASE


Mass: 35520.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P52279, prolyl aminopeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSER 110 IS ARRANGED IN A SHARP GAMMA-TURN AND EXHIBITS AN ENERGETICALLY UNFAVORABLE CONFORMATION, ...SER 110 IS ARRANGED IN A SHARP GAMMA-TURN AND EXHIBITS AN ENERGETICALLY UNFAVORABLE CONFORMATION, IN THE RAMACHANDRAN PLOT THIS CORRESPONDS TO ONLY A GENEROUSLY ALLOWED REGION, BUT IS DEFINED BY CLEAR DENSITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMTris-HCl1reservoir
30.02 %(w/v)sodium azide1reservoir

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Data collection

DiffractionMean temperature: 260 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 29854 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.096
Reflection
*PLUS
Num. measured all: 154900

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→7 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 -10 %RANDOM
Rwork0.192 ---
obs0.192 26672 94.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6140 0 0 199 6339
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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