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- PDB-6f2h: Structure of Protease 1 from Pyrococcus horikoshii co-crystallize... -

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Basic information

Entry
Database: PDB / ID: 6f2h
TitleStructure of Protease 1 from Pyrococcus horikoshii co-crystallized in presence of 10 mM Tb-Xo4 and potassium iodide.
ComponentsDeglycase PH1704
KeywordsHYDROLASE / Tb-Xo4 / crystallophore / nucleation / phasing / Protease
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
Tb-Xo4 / IODIDE ION / TERBIUM(III) ION / Deglycase PH1704
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.19 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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
D: Deglycase PH1704
E: Deglycase PH1704
F: Deglycase PH1704
G: Deglycase PH1704
H: Deglycase PH1704
I: Deglycase PH1704
J: Deglycase PH1704
K: Deglycase PH1704
L: Deglycase PH1704
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,63841
Polymers223,80512
Non-polymers7,83329
Water13,331740
1
A: Deglycase PH1704
B: Deglycase PH1704
C: Deglycase PH1704
D: Deglycase PH1704
E: Deglycase PH1704
F: Deglycase PH1704
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,71621
Polymers111,9036
Non-polymers3,81315
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Deglycase PH1704
H: Deglycase PH1704
I: Deglycase PH1704
J: Deglycase PH1704
K: Deglycase PH1704
L: Deglycase PH1704
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,92220
Polymers111,9036
Non-polymers4,02014
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.577, 84.698, 144.343
Angle α, β, γ (deg.)90.00, 90.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18650.418 Da / Num. of mol.: 12
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
#2: Chemical
ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Tb
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis tris propane pH 7, 20 to 30% PEG3350, Potassium Iodide 200 mM. Tb-Xo4 was directly mixed with the protein solution at a final concentration of 10 mM prior to crystallization.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.6492 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6492 Å / Relative weight: 1
ReflectionResolution: 2.19→46.01 Å / Num. obs: 101279 / % possible obs: 99.12 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.94 Å2 / Rpim(I) all: 0.072 / Net I/σ(I): 11.43
Reflection shellHighest resolution: 2.19 Å / Rpim(I) all: 0.447

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementResolution: 2.19→46.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.193 5027 4.97 %RANDOM
Rwork0.15 ---
obs0.152 101079 98.6 %-
Displacement parametersBiso mean: 40.97 Å2
Baniso -1Baniso -2Baniso -3
1--8.4603 Å20 Å2-0.9218 Å2
2--4.8402 Å20 Å2
3---3.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 2.19→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15768 0 290 764 16822
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132357HARMONIC4
X-RAY DIFFRACTIONt_angle_deg0.9158633HARMONIC4
X-RAY DIFFRACTIONt_dihedral_angle_d7068SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes372HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4565HARMONIC5
X-RAY DIFFRACTIONt_it32357HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.69
X-RAY DIFFRACTIONt_other_torsion14.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1992SEMIHARMONIC5
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_contact36626SEMIHARMONIC4
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2824 321 5.12 %
Rwork0.2123 5954 -
all0.2157 6275 -
obs--83.52 %
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)
10.8415-0.04670.02870.9204-0.22142.2044-0.03550.05540.01060.0448-0.0103-0.1321-0.2734-0.11970.04580.02230.03060.0013-0.03890.015-0.094314.735755.40739.7353
20.9362-0.3542-0.22241.74490.25251.4896-0.04890.0031-0.02880.19710.0061-0.06170.1723-0.19220.04280.0581-0.02410.0173-0.04870.0027-0.120515.280530.746827.9016
30.8325-0.2454-0.08451.74340.64351.27270.01280.01140.03940.10470.0838-0.13750.11810.081-0.09650.00380.0227-0.0368-0.11390.00080.004136.526813.583616.1104
41.12210.02250.07341.1517-0.38892.0324-0.0010.0349-0.0711-0.01780.0234-0.06550.0678-0.0885-0.02240.0150.03380.0213-0.1217-0.0071-0.014525.38853.4742-10.7496
51.0997-0.2661-0.12131.8053-0.32241.3248-0.05090.015-0.0295-0.09860.0215-0.04050.09710.03370.02940.0445-0.01760.018-0.0517-0.0127-0.102925.362527.5978-28.0874
60.4384-0.01490.06591.37380.59481.93960.0170.0256-0.0511-0.072-0.0880.0205-0.0558-0.34480.0711-0.04160.0242-0.01850.07560.0072-0.12343.552845.4926-15.9474
70.95830.21770.32421.99280.23391.40930.00890.00050.0851-0.0481-0.02290.1429-0.06750.00090.0140.01420.0563-0.0093-0.06580.0005-0.069512.3532-17.364945.0616
80.69870.59160.58961.48190.64222.1424-0.02950.0709-0.0152-0.0026-0.00910.0316-0.15160.24340.03860.0454-0.0553-0.0348-0.07940.0671-0.071930.84544.149253.7664
90.78770.1777-0.45840.8926-0.39032.2911-0.01430.0385-0.01660.0484-0.04620.0035-0.2431-0.07850.06040.1659-0.0085-0.059-0.183-0.0239-0.076120.768411.674881.8699
100.76420.33280.27671.8124-0.21660.7846-0.0259-0.04580.01950.0980.0047-0.0995-0.13130.06030.02120.0711-0.0281-0.0386-0.0574-0.0173-0.095727.8385-11.376199.2396
110.9410.0130.40761.3562-0.31582.93120.0152-0.02220.11590.03750.0688-0.01350.185-0.2021-0.0839-0.0052-0.03860.0119-0.00660.0328-0.1379.1276-33.86490.0274
120.7773-0.0476-0.08070.327-0.52342.66020.0343-0.03510.1122-0.0079-0.02830.02920.38060.2008-0.00610.17220.0885-0.0198-0.0839-0.0056-0.195819.254-41.057163.0907
13-0.0009-0.07020.02420.4726-0.5370.2304-0.0189-0.0223-0.00540.00640.0094-0.02820.0032-0.00710.0095-0.00230.0058-0.00550.001-0.03260.01916.37236.776440.1202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ N|* }

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