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- PDB-6iru: Crystal structure of Peptidase E from Deinococcus radiodurans in ... -

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Basic information

Entry
Database: PDB / ID: 6iru
TitleCrystal structure of Peptidase E from Deinococcus radiodurans in P6422 space group
Componentspeptidase DR_1070
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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYadav, P. / Chandravanshi, K. / Kumar, A. / 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
DepositionNov 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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 DR_1070
B: peptidase DR_1070
C: peptidase DR_1070


Theoretical massNumber of molelcules
Total (without water)68,1893
Polymers68,1893
Non-polymers00
Water1448
1
A: peptidase DR_1070

A: peptidase DR_1070


Theoretical massNumber of molelcules
Total (without water)45,4602
Polymers45,4602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area15630 Å2
MethodPISA
2
B: peptidase DR_1070
C: peptidase DR_1070


Theoretical massNumber of molelcules
Total (without water)45,4602
Polymers45,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.745, 166.745, 100.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein peptidase DR_1070


Mass: 22729.799 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_1070 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9RVF9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.69 Å3/Da / Density meas: 54.32 Mg/m3 / Density % sol: 58.57 % / Description: hexagonal shape (200-250 micron)
Crystal growTemperature: 294 K / Method: microbatch / pH: 6.5 / Details: 0.1 M Bis-tris pH 6.5, 25 % PEG3350 / PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9778 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2018 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.7→48.14 Å / Num. obs: 23227 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 58.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.028 / Rrim(I) all: 0.11 / Net I/σ(I): 23.5
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.147 / Num. unique obs: 3029 / CC1/2: 0.909 / Rpim(I) all: 0.297 / Rrim(I) all: 1.186 / % 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: 6A4T

6a4t


Resolution: 2.7→16.026 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.68
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1157 5.02 %random selection
Rwork0.214 ---
obs0.2161 23053 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64 Å2
Refinement stepCycle: LAST / Resolution: 2.7→16.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 0 8 4406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064481
X-RAY DIFFRACTIONf_angle_d0.876140
X-RAY DIFFRACTIONf_dihedral_angle_d3.0252649
X-RAY DIFFRACTIONf_chiral_restr0.055751
X-RAY DIFFRACTIONf_plane_restr0.007795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.82230.33861530.29482673X-RAY DIFFRACTION100
2.8223-2.97030.31841480.27362670X-RAY DIFFRACTION100
2.9703-3.1550.31321210.26522721X-RAY DIFFRACTION100
3.155-3.39650.32111490.2612698X-RAY DIFFRACTION100
3.3965-3.73440.26341390.23682724X-RAY DIFFRACTION100
3.7344-4.26580.24351340.19132744X-RAY DIFFRACTION100
4.2658-5.34120.21851500.17552775X-RAY DIFFRACTION100
5.3412-16.02630.2261630.19472891X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.4828 Å / Origin y: -67.2766 Å / Origin z: 11.1551 Å
111213212223313233
T0.3885 Å2-0.0733 Å2-0.0259 Å2-0.601 Å2-0.0389 Å2--0.4079 Å2
L1.3427 °2-0.438 °20.1413 °2-0.4039 °2-0.149 °2--0.7784 °2
S-0.1605 Å °-0.1169 Å °0.0444 Å °0.0843 Å °0.0713 Å °0.1016 Å °-0.0778 Å °-0.3418 Å °0.0908 Å °
Refinement TLS groupSelection details: all

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