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- PDB-1xrl: Crystal structure of active site F1-mutant Y205F complex with inh... -

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Basic information

Entry
Database: PDB / ID: 1xrl
TitleCrystal structure of active site F1-mutant Y205F complex with inhibitor PCK
ComponentsProline iminopeptidase
KeywordsHYDROLASE / ALPHA-BETA HYDROLASE / CAGED ACTIVE SITE / SUBSTRATE RECOGNITION / HYDROGEN BONDED NETWORK / CHLOROMETHYL KETONE INHIBITOR
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
(2R,3S)-3-AMINO-1-CHLORO-4-PHENYL-BUTAN-2-OL / Proline iminopeptidase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7142
Polymers33,5141
Non-polymers2001
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.330, 61.850, 80.770
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: 33514.090 Da / Num. of mol.: 1 / Mutation: Y205F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA0830 / Plasmid: PRSET6C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL / References: UniProt: P96084, prolyl aminopeptidase
#2: Chemical ChemComp-PHK / (2R,3S)-3-AMINO-1-CHLORO-4-PHENYL-BUTAN-2-OL


Mass: 199.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14ClNO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.18 Å3/Da / Density % sol: 43.18 %
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: 1.82→19.4 Å / Num. all: 25780 / Num. obs: 24988 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 17 Å2 / Net I/σ(I): 15
Reflection shellResolution: 1.82→1.91 Å / % possible all: 61.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→19.4 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 416355.66 / 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
Rfree0.279 1133 4.8 %RANDOM
Rwork0.241 ---
all0.257 24856 --
obs0.241 23723 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.2672 Å2 / ksol: 0.383364 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--7.69 Å20 Å2
3----8.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.82→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 13 118 2462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
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: 1.82→1.91 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 127 4.7 %
Rwork0.338 2603 -
obs--61.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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