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- PDB-1fno: PEPTIDASE T (TRIPEPTIDASE) -

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Basic information

Entry
Database: PDB / ID: 1fno
TitlePEPTIDASE T (TRIPEPTIDASE)
ComponentsPEPTIDASE T
KeywordsHYDROLASE / metallo peptidase / protease
Function / homology
Function and homology information


tripeptide aminopeptidase activity / tripeptide aminopeptidase / peptide catabolic process / metallopeptidase activity / proteolysis / zinc ion binding / cytosol
Similarity search - Function
Peptidase M20B, tripeptide aminopeptidase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 ...Peptidase M20B, tripeptide aminopeptidase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsHakansson, K. / Miller, C.G.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Structure of Peptidase T from Salmonella typhimurium
Authors: Hakansson, K. / Miller, C.G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization of Peptidase T from Salmonella typhimurium
Authors: Hakansson, K. / Broder, D. / Wang, A.H. / Miller, C.G.
History
DepositionAug 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDASE T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0035
Polymers46,6801
Non-polymers3234
Water2,342130
1
A: PEPTIDASE T
hetero molecules

A: PEPTIDASE T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,00510
Polymers93,3602
Non-polymers6468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3790 Å2
ΔGint-233 kcal/mol
Surface area33800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.374, 46.036, 96.591
Angle α, β, γ (deg.)90.00, 116.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-642-

HOH

DetailsThe biological assembly is probably a dimer constructed from chain A and a symmetry partner generated by the two-fold symmetry.

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Components

#1: Protein PEPTIDASE T / AMINOTRIPEPTIDASE / TRIPEPTIDASE


Mass: 46679.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P26311, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293 K / Method: vapor equilibration / pH: 7.5
Details: 10 mg/ml enzyme in 10 mM Tris pH 7.5 mixed with an equal amount and equilibrated against 50mM Tris pH 7.5, 1.2 M ammonium sulfate, vapor equilibration, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Hakansson, K., (2000) Acta Crystallogr., Sect.D, 56, 924.
PH range low: 9 / PH range high: 7
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDDetails
1sodium potassium tartrate1reservoiror ammonium sulfate
2Bis-Tris1reservoiror Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9879
DetectorType: ADSC / Detector: CCD / Date: Sep 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 20598 / % possible obs: 99.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.246 / Num. unique all: 2019 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 99755
Reflection shell
*PLUS
% possible obs: 99.2 % / Mean I/σ(I) obs: 6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→500 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1021 -freerflag (CCP4)
Rwork0.222 ---
all-20803 --
obs-20578 98.9 %-
Refinement stepCycle: LAST / Resolution: 2.4→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 12 130 3260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.68
X-RAY DIFFRACTIONc_torsion_deg25
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 500 Å / σ(F): 0 / Rfactor obs: 0.224 / Rfactor Rfree: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_d / Dev ideal: 1.7

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