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- PDB-2vrn: The structure of the stress response protein DR1199 from Deinococ... -

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Basic information

Entry
Database: PDB / ID: 2vrn
TitleThe structure of the stress response protein DR1199 from Deinococcus radiodurans: a member of the DJ-1 superfamily
ComponentsPROTEASE I
KeywordsHYDROLASE / CYSTEINE SULFENIC ACID / DJ-1/THIJ/PFPI SUPERFAMILY / PROTEASE / STRESS RESPONSE
Function / homology
Function and homology information


peptidase activity / proteolysis / metal ion binding
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
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFioravanti, E. / Dura, M.A. / Lascoux, D. / Micossi, E. / McSweeney, S.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of the stress response protein DR1199 from Deinococcus radiodurans: a member of the DJ-1 superfamily.
Authors: Fioravanti, E. / Dura, M.A. / Lascoux, D. / Micossi, E. / Franzetti, B. / McSweeney, S.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 11, 2012Group: Other
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_id_ISSN ..._audit_author.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASE I
B: PROTEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4213
Polymers41,3972
Non-polymers241
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-22.9 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.838, 88.562, 64.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEASE I / DR1199


Mass: 20698.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CYSTEINE 115 MODIFIED TO CYSTEINE SULFENIC ACID (CSO)
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RV31
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.23 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 5.9 / Details: 0.2 M MAGNESIUM FORMATE PH 5.9, 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 20998 / % possible obs: 99.8 % / Observed criterion σ(I): 4 / Redundancy: 6.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.5
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSI

1gsi


Resolution: 2.15→19.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.11 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAIN ATOMS WITHOUT VISIBLE ELECTRON DENSITY AT 1. 0 SIGMA WERE REMOVED FROM THE MODEL. A PEAK TO 6.0 SIGMA (POSSIBLY AN ION) NEAR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAIN ATOMS WITHOUT VISIBLE ELECTRON DENSITY AT 1. 0 SIGMA WERE REMOVED FROM THE MODEL. A PEAK TO 6.0 SIGMA (POSSIBLY AN ION) NEAR RESIDUES A22 AND A59 WAS NOT MODELLED DUE TO LACK OF COORDINATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1077 5.1 %RANDOM
Rwork0.2 ---
obs0.203 19890 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 1 172 2951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222868
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9823894
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3325.603116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39215496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7461513
X-RAY DIFFRACTIONr_chiral_restr0.0870.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022153
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21404
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21934
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4351.51921
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72822981
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32231087
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9134.5913
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 72
Rwork0.269 1435
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)
12.14490.1461.47055.27061.14323.78420.2817-0.2167-0.30260.9850.4289-0.77760.7370.1055-0.71060.16220.0889-0.18860.125-0.12340.219820.84532.171835.5637
22.8796-0.5224-1.119712.0416.054611.03940.2569-0.2985-0.28971.31840.1683-0.14921.0529-0.5679-0.42520.13630.0389-0.16530.24520.04280.149615.6482.39136.1677
33.3096-0.91060.63046.14872.94717.63820.2101-0.2026-0.24860.03330.0988-0.13-0.1324-0.3646-0.30890.0522-0.00490.00110.2142-0.03660.167411.567410.843830.4377
43.2201-0.04070.54113.4721.52784.7544-0.0403-0.0230.22550.06280.289-0.4443-0.30350.121-0.24870.0414-0.0086-0.00620.1196-0.10620.188418.884418.265830.4403
53.1974-0.01211.94072.48930.72183.8902-0.13940.290.3636-0.13470.5-0.8485-0.13230.6743-0.3606-0.0314-0.03670.03890.1552-0.26650.364126.938618.34328.7021
69.8531-6.0761-2.42515.0615.017411.6171-0.4115-0.33050.64491.10791.033-1.43030.25170.5022-0.62150.12950.0625-0.22880.07-0.3080.258426.344718.005843.3235
72.24510.26760.6582.74760.09964.27880.22130.581-0.1263-0.67270.1146-0.3415-0.17650.3634-0.33590.34170.04090.11060.2127-0.06390.074710.51364.47111.3462
89.1945-3.2269-1.40849.10283.503510.65270.42830.324-0.5877-0.1637-0.0056-0.05340.36360.5606-0.42270.08170.0658-0.07190.0049-0.18740.143214.0438-3.33469.7778
93.7818-0.3092.7371.53892.41496.5801-0.00640.60870.1895-0.87240.1969-0.5539-0.77761.1886-0.19040.342-0.11120.2280.1538-0.0360.00116.429711.61192.5387
1017.8292-13.1117.717220.1535-6.87722.3222-0.7570.15721.0357-0.98750.5731-0.849-1.14670.78080.18390.6759-0.27740.33130.33660.15770.182715.769820.60521.2796
113.41480.781.71074.49512.09234.6856-0.0308-0.03780.4259-0.3728-0.10930.1201-0.4963-0.06630.14010.18860.03930.03360.06720.00580.06154.114616.896112.5296
1214.130911.4634-6.059623.2712-4.19534.8807-0.18220.43592.0174-1.62340.45831.1715-1.2989-0.3338-0.27610.81560.0932-0.1120.3780.03240.3070.472818.6602-2.0935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 54
2X-RAY DIFFRACTION2A55 - 80
3X-RAY DIFFRACTION3A81 - 102
4X-RAY DIFFRACTION4A103 - 140
5X-RAY DIFFRACTION5A141 - 173
6X-RAY DIFFRACTION6A174 - 190
7X-RAY DIFFRACTION7B6 - 54
8X-RAY DIFFRACTION8B55 - 63
9X-RAY DIFFRACTION9B64 - 93
10X-RAY DIFFRACTION10B94 - 109
11X-RAY DIFFRACTION11B110 - 172
12X-RAY DIFFRACTION12B173 - 190

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