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- PDB-6f2f: Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cys... -

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Basic information

Entry
Database: PDB / ID: 6f2f
TitleCrystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate.
ComponentsDeglycase PH1704
KeywordsCELL CYCLE / Lanthanide complexes / Tb-Xo4 / Crystallophore / Phasing / nucleation
Function / homology
Function and homology information


protein deglycase / protein deglycase activity / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytoplasm
Similarity search - Function
: / Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydroxyacetone / Tb-Xo4 / TERBIUM(III) ION / Deglycase PH1704
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEngilberge, S. / Riobe, F. / Di Pietro, S. / Franzetti, B. / Girard, E. / Dumont, E. / Maury, O.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BS07-0007-01 France
CitationJournal: Chemistry / Year: 2018
Title: Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.
Authors: Engilberge, S. / Riobe, F. / Wagner, T. / Di Pietro, S. / Breyton, C. / Franzetti, B. / Shima, S. / Girard, E. / Dumont, E. / Maury, O.
History
DepositionNov 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jul 8, 2020Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _pdbx_entity_nonpoly.name
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deglycase PH1704
B: Deglycase PH1704
C: Deglycase PH1704
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,63816
Polymers55,9513
Non-polymers2,68713
Water11,061614
1
A: Deglycase PH1704
B: Deglycase PH1704
C: Deglycase PH1704
hetero molecules

A: Deglycase PH1704
B: Deglycase PH1704
C: Deglycase PH1704
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,27632
Polymers111,9036
Non-polymers5,37326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)124.588, 124.588, 128.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Sugars , 2 types, 4 molecules ABC

#1: Protein Deglycase PH1704 / Intracellular protease PH1704 / Protease 1


Mass: 18650.418 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1704 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O59413, protein deglycase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#5: Sugar ChemComp-2HA / Dihydroxyacetone


Type: saccharide / Mass: 90.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H6O3

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Non-polymers , 4 types, 626 molecules

#2: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tb
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.9 to 2.4 ammonium sulfate, 0.2 M sodium potassium tartrate, 100 mM trisodium citrate dehydrate pH 5.6. 10 mM Tb-Xo4 were solubilized with the protein solution prior to perform crystallization drops.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97974 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97974 Å / Relative weight: 1
ReflectionResolution: 1.65→44.77 Å / Num. obs: 121190 / % possible obs: 99.8 % / Redundancy: 11.5 % / Biso Wilson estimate: 25.59 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G2I

1g2i


Resolution: 1.65→44.77 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.055
RfactorNum. reflection% reflectionSelection details
Rfree0.17 6066 5.01 %RANDOM
Rwork0.161 ---
obs0.161 121190 99.7 %-
Displacement parametersBiso mean: 29.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.2668 Å20 Å20 Å2
2--2.2668 Å20 Å2
3----4.5335 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.65→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 137 623 4702
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018261HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0514969HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1800SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1173HARMONIC5
X-RAY DIFFRACTIONt_it8261HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.57
X-RAY DIFFRACTIONt_other_torsion12.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion505SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9694SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2293 432 5.05 %
Rwork0.2233 8116 -
all0.2236 8548 -
obs--96.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.39060.1752-0.36950.64780.12740.8081-0.03750.2478-0.0321-0.05790.0334-0.0290.0276-0.0130.004-0.087-0.0214-0.00160.0031-0.0206-0.075633.866226.6453-14.5275
21.7920.5855-0.25350.77910.04380.3718-0.05670.0839-0.2702-0.00240.013-0.10820.0635-0.02280.0437-0.11750.0060.02670.0075-0.028-0.064263.371429.8469-14.9588
30.9164-0.1233-0.42041.26860.6741.12710.07520.07830.1672-0.13570.0128-0.0513-0.2334-0.0444-0.088-0.06150.03470.0399-0.02930.005-0.089667.853960.5357-13.8118
41.1157-0.59930.01650.4496-0.59940-0.00560.01410.04660.20480.02070.2318-0.08570.1819-0.0151-0.07780.0061-0.07030.0969-0.0796-0.04848.825145.1621-9.7708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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