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- PDB-2cf4: Pyrococcus horikoshii TET1 peptidase can assemble into a tetrahed... -

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Basic information

Entry
Database: PDB / ID: 2cf4
TitlePyrococcus horikoshii TET1 peptidase can assemble into a tetrahedron or a large octahedral shell
ComponentsPROTEIN PH0519
KeywordsHYDROLASE / AMINOPEPTIDASE / METALLOPROTEIN / HYPERTHERMOPHILE / ARCHAEA / TETRAHEDRAL
Function / homology
Function and homology information


aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized protein
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsVellieux, F.M.D. / Schoehn, G. / Dura, M.A. / Roussel, A. / Franzetti, B.
Citation
Journal: J Biol Chem / Year: 2006
Title: An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.
Authors: Guy Schoehn / Frédéric M D Vellieux / M Asunción Durá / Véronique Receveur-Bréchot / Céline M S Fabry / Rob W H Ruigrok / Christine Ebel / Alain Roussel / Bruno Franzetti /
Abstract: Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea ...Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea Pyrococcus horikoshii (PhTET1) was found to assemble as a 12-subunit tetrahedron and as a 24-subunit octahedral particle. Both quaternary structures were solved by combining x-ray crystallography and cryoelectron microscopy data. The internal organization of the PhTET1 particles reveals highly self-compartmentalized systems made of networks of access channels extended by vast catalytic chambers. The two edifices display aminopeptidase activity, and their organizations indicate substrate navigation mechanisms different from those described in other large peptidase complexes. Compared with the tetrahedron, the octahedron forms a more expanded hollow structure, representing a new type of giant peptidase complex. PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids.
#1: Journal: Embo J. / Year: 2002
Title: Tetrahedral Aminopeptidase: A Novel Large Protease Complex from Archaea
Authors: Franzetti, B. / Schoehn, G. / Hernandez, J.F. / Jaquinod, M. / Ruigrok, R.W. / Zaccai, G.
History
DepositionFeb 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN PH0519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3253
Polymers37,2071
Non-polymers1182
Water0
1
A: PROTEIN PH0519
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)447,89936
Polymers446,48512
Non-polymers1,41424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation34_555-y+1/2,z,-x+1/21
crystal symmetry operation55_555-z+1/2,-x+1/2,y1
crystal symmetry operation26_655-x+1,-y,z1
crystal symmetry operation11_555y+1/2,-z,-x+1/21
crystal symmetry operation77_545z+1/2,x-1/2,y1
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation8_545-z+1/2,x-1/2,-y1
crystal symmetry operation30_555z+1/2,-x+1/2,-y1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation75_655-x+1,y,-z1
crystal symmetry operation84_554-y+1/2,-z,x-1/21
MethodPQS
Unit cell
Length a, b, c (Å)221.880, 221.880, 221.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein PROTEIN PH0519 / PHTET1-12S


Mass: 37207.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Strain: OT3 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O58255, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co

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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: 2.7 Å3/Da / Density % sol: 52 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9797
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.08→26.91 Å / Num. obs: 8651 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 79.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 31
Reflection shellResolution: 3.08→3.25 Å / Redundancy: 9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5 / % possible all: 75.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
SELDATdata scaling
SCALKB2data scaling
KBAPLYdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHE

1vhe


Resolution: 3.08→26.91 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 153864.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.332 458 5.3 %RANDOM
Rwork0.256 ---
obs0.256 8651 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.5319 Å2 / ksol: 0.270863 e/Å3
Displacement parametersBiso mean: 60.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a1.03 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 3.08→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 2 0 2590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.750.65
X-RAY DIFFRACTIONc_mcangle_it1.411.2
X-RAY DIFFRACTIONc_scbond_it0.220.4
X-RAY DIFFRACTIONc_scangle_it0.620.75
LS refinement shellResolution: 3.08→3.2 Å / Rfactor Rfree error: 0.09 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.49 30 5.1 %
Rwork0.362 564 -
obs--67.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_JPP.PARAMPROTEIN_JPP.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM

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