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- PDB-1mtz: Crystal Structure of the Tricorn Interacting Factor F1 -

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Basic information

Entry
Database: PDB / ID: 1mtz
TitleCrystal Structure of the Tricorn Interacting Factor F1
ComponentsProline iminopeptidase
KeywordsHYDROLASE / ALPHA-BETA HYDROLASE / CAP DOMAIN / CAGED ACTIVE SITE / PROLYL PEPTIDASE
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 iminopeptidase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoettig, P. / Groll, M. / Kim, J.-S. / Huber, R. / Brandstetter, H.
CitationJournal: Embo J. / Year: 2002
Title: Structures of the tricorn-interacting aminopeptidase F1 with different ligands explain its catalytic mechanism
Authors: Goettig, P. / Groll, M. / Kim, J.-S. / Huber, R. / Brandstetter, H.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline iminopeptidase


Theoretical massNumber of molelcules
Total (without water)33,5301
Polymers33,5301
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.961, 57.095, 82.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the monomer in the asymmetric unit

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Components

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


Mass: 33530.090 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8000, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
2100 mMMES1reservoirpH6.0
3100 mMBis-Tris-HCl1reservoirpH6.0
47-12 %PEG60001reservoir
5100 mMHEPES1reservoirpH7.5
620 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2001 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 23078 / Num. obs: 23078 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.6 Å2 / Net I/σ(I): 9.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 22463

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MT3

1mt3


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2207 -RANDOM
Rwork0.199 ---
all0.236 23078 --
obs0.236 22449 91.2 %-
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20 Å2
2---0.66 Å20 Å2
3----1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å-
Luzzati d res low-20 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 0 179 2507
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.21
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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