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- PDB-6hf6: Crystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 6hf6
TitleCrystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococcus horikoshii co-crystallized with Tb-Xo4.
ComponentsDeglycase PH1704
KeywordsHYDROLASE / meshandcollect / de novo phasing / SAD / crystallization / Tb-Xo4 / crystallophore / Lanthanide complex / multi-crystals data collection / ccCluster
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 / MALONATE ION / TERBIUM(III) ION / Deglycase PH1704
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsEngilberge, S. / Wagner, T. / Santoni, G. / Breyton, C. / Shima, S. / Franzetti, B. / Riobe, F. / Maury, O. / Girard, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: J.Appl.Crystallogr. / Year: 2019
Title: Protein crystal structure determination with the crystallophore, a nucleating and phasing agent.
Authors: Engilberge, S. / Wagner, T. / Santoni, G. / Breyton, C. / Shima, S. / Franzetti, B. / Riobe, F. / Maury, O. / Girard, E.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 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.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_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.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.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)58,04013
Polymers55,4293
Non-polymers2,61110
Water9,944552
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)116,08026
Polymers110,8586
Non-polymers5,22220
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12160 Å2
ΔGint-46 kcal/mol
Surface area34480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.620, 124.620, 130.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Deglycase PH1704 / Intracellular protease PH1704


Mass: 18476.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1704 / Production host: Escherichia coli (E. coli)
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.: 3 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Tb
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 295 K / Method: vapor diffusion, hanging drop
Details: Protein concentration : 10 mg.ml-1 Crystallization drop : 1.5 ul of protein and 1.5 ul of the precipitant. Crystallization solution : 2.8 to 3.4 Sodium malonate pH 5.5. Note : Tb-Xo4 was ...Details: Protein concentration : 10 mg.ml-1 Crystallization drop : 1.5 ul of protein and 1.5 ul of the precipitant. Crystallization solution : 2.8 to 3.4 Sodium malonate pH 5.5. Note : Tb-Xo4 was solubilized with the protein solution for a final concentration of 10 mM, 1 hour before to perform the crystallization drop.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.648 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.648 Å / Relative weight: 1
ReflectionResolution: 2→19.99 Å / Num. obs: 69275 / % possible obs: 99.5 % / Redundancy: 18.2 % / Biso Wilson estimate: 30.61 Å2 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.036 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.04 Å / Rpim(I) all: 0.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3384 4.89 %RANDOM
Rwork0.162 ---
obs0.163 69185 99.4 %-
Displacement parametersBiso mean: 39.54 Å2
Baniso -1Baniso -2Baniso -3
1-8.5527 Å20 Å20 Å2
2--8.5527 Å20 Å2
3----17.1053 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 115 553 4574
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018146HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9914760HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1770SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1258HARMONIC5
X-RAY DIFFRACTIONt_it8146HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion14.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion503SEMIHARMONIC5
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_contact9149SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2051 249 4.92 %
Rwork0.2033 4816 -
all0.2034 5065 -
obs--99.22 %
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)
11.7212-0.038-0.41470.92920.10330.5284-0.01850.2919-0.0855-0.06430.0286-0.01790.0183-0.0044-0.0102-0.1402-0.0184-0.016-0.043-0.0549-0.001833.797426.4045-14.488
22.19060.4554-0.16731.06610.05570.9098-0.06160.1283-0.1511-0.00650.0171-0.05520.0282-0.00750.0445-0.1629-0.00090.0173-0.0647-0.04930.022463.381629.7272-14.9103
31.2274-0.3034-0.43651.59820.84741.39730.13370.0660.4467-0.17440.0840.0034-0.24630.0124-0.2177-0.17320.00610.0883-0.15680.00560.223567.710560.3439-13.8824
42.3279-0.98440.1940.3483-0.17660.1307-0.00440.05970.16590.10810.04610.1347-0.1980.2399-0.0417-0.09640.0265-0.07-0.058-0.14930.035948.691244.9728-9.8334
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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