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- PDB-1xrp: Crystal structure of active site F1-mutant E213Q soaked with pept... -

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Basic information

Entry
Database: PDB / ID: 1xrp
TitleCrystal structure of active site F1-mutant E213Q soaked with peptide Pro-Leu-Gly-Gly
Components
  • PLGG
  • Proline iminopeptidase
KeywordsHYDROLASE / ALPHA-BETA HYDROLASE / CAGED ACTIVE SITE / SUBSTRATE RECOGNITION / HYDROGEN BONDED NETWORK / PEPTIDE CLEAVAGE
Function / homology
Function and homology information


prolyl aminopeptidase / aminopeptidase activity / proteolysis / membrane
Similarity search - Function
Proline-specific peptidase / Peptidase S33 / Serine aminopeptidase, 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 / Proline iminopeptidase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGoettig, P. / Brandstetter, H. / Groll, M. / Goehring, W. / Konarev, P.V. / Svergun, D.I. / Huber, R. / Kim, J.-S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum
Authors: Goettig, P. / Brandstetter, H. / Groll, M. / Goehring, W. / Konarev, P.V. / Svergun, D.I. / Huber, R. / Kim, J.-S.
History
DepositionOct 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline iminopeptidase
Q: PLGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9873
Polymers33,8712
Non-polymers1151
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-7 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.420, 60.520, 79.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proline iminopeptidase / PIP / Prolyl aminopeptidase / PAP / Tricorn protease interacting factor F1


Mass: 33529.105 Da / Num. of mol.: 1 / Mutation: E213Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA0830 / Plasmid: PRSET6C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P96084, prolyl aminopeptidase
#2: Protein/peptide PLGG


Mass: 342.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.84 Å3/Da / Density % sol: 32.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2003
RadiationMonochromator: Si 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.2→13 Å / Num. all: 11541 / Num. obs: 11237 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 13.5 Å2 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.44 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→12.97 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 296082.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 487 5.1 %RANDOM
Rwork0.22 ---
all0.239 9949 --
obs0.22 9462 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4625 Å2 / ksol: 0.394043 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-23.51 Å20 Å20 Å2
2---11.2 Å20 Å2
3----12.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→12.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 8 119 2483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 79 5.2 %
Rwork0.303 1444 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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