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- PDB-6a4t: Crystal structure of Peptidase E from Deinococcus radiodurans R1 -

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Basic information

Entry
Database: PDB / ID: 6a4t
TitleCrystal structure of Peptidase E from Deinococcus radiodurans R1
ComponentsPeptidase EDipeptidase E
KeywordsHYDROLASE / S51 peptidase / peptidase E / dimer / active site / esterase
Function / homologyPeptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase-like / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / Uncharacterized peptidase DR_1070
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYadav, P. / Goyal, V.G. / Kumar, A. / Gokhale, S.M. / Makde, R.D.
CitationJournal: Proteins / Year: 2019
Title: Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability.
Authors: Yadav, P. / Goyal, V.D. / Chandravanshi, K. / Kumar, A. / Gokhale, S.M. / Jamdar, S.N. / Makde, R.D.
History
DepositionJun 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase E
B: Peptidase E


Theoretical massNumber of molelcules
Total (without water)47,4622
Polymers47,4622
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, protein elutes as symmetric peak on Superdex 200 column that corresponds to molecular mass of dimer (approx. 45 kDa)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-14 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.417, 95.417, 92.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-262-

HOH

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Components

#1: Protein Peptidase E / Dipeptidase E


Mass: 23730.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Gene: DR_1070 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9RVF9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 7.5
Details: 0.1 M Tris-Cl pH 7.5, 0.2 M magnesium chloride, 22 % PEG 8000
PH range: 6-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 22, 2014 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2→47.71 Å / Num. obs: 29488 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 25.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.034 / Rrim(I) all: 0.105 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 3 / Num. unique obs: 2138 / CC1/2: 0.926 / Rpim(I) all: 0.254 / Rrim(I) all: 0.79 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4E

3l4e


Resolution: 2→47.709 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 1452 4.95 %Random selection
Rwork0.2733 ---
obs0.2746 29352 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2→47.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 0 228 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022967
X-RAY DIFFRACTIONf_angle_d0.5684039
X-RAY DIFFRACTIONf_dihedral_angle_d9.8221781
X-RAY DIFFRACTIONf_chiral_restr0.041480
X-RAY DIFFRACTIONf_plane_restr0.004522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.35631450.29992748X-RAY DIFFRACTION100
2.0715-2.15440.32761250.29562740X-RAY DIFFRACTION100
2.1544-2.25250.29131580.30072759X-RAY DIFFRACTION100
2.2525-2.37120.33491240.28542778X-RAY DIFFRACTION100
2.3712-2.51980.31811530.28882719X-RAY DIFFRACTION100
2.5198-2.71430.30661480.2992777X-RAY DIFFRACTION100
2.7143-2.98750.30551530.29292764X-RAY DIFFRACTION100
2.9875-3.41970.33831370.27692814X-RAY DIFFRACTION100
3.4197-4.3080.25511580.24132825X-RAY DIFFRACTION100
4.308-47.72210.28341510.25642976X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 39.4804 Å / Origin y: -8.0825 Å / Origin z: -19.2706 Å
111213212223313233
T0.1892 Å2-0.007 Å20.0098 Å2-0.1855 Å20.0152 Å2--0.1591 Å2
L1.0451 °2-0.6978 °2-0.0251 °2-1.2087 °20.089 °2--0.534 °2
S-0.0334 Å °0.054 Å °-0.0389 Å °0.0699 Å °-0.0185 Å °0.0215 Å °0.0265 Å °-0.0207 Å °0.0465 Å °
Refinement TLS groupSelection details: all

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