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- PDB-6a4r: Crystal structure of aspartate bound peptidase E from Salmonella ... -

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Basic information

Entry
Database: PDB / ID: 6a4r
TitleCrystal structure of aspartate bound peptidase E from Salmonella enterica
ComponentsPeptidase E
KeywordsHYDROLASE / S51 peptidase / peptidase E / dimer / active site / active site loop
Function / homology
Function and homology information


dipeptidase E / dipeptidase activity / serine-type peptidase activity / proteolysis / cytoplasm
Similarity search - Function
Peptidase S51, dipeptidase E / Peptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / Peptidase E
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.828 Å
AuthorsYadav, P. / Chandravanshi, K. / Goyal, V.D. / Singh, R. / Kumar, A. / Gokhale, S.M. / Makde, R.D.
CitationJournal: FEBS Lett. / Year: 2018
Title: Structure of Asp-bound peptidase E from Salmonella enterica: Active site at dimer interface illuminates Asp recognition.
Authors: Yadav, P. / Goyal, V.D. / Gaur, N.K. / Kumar, A. / Gokhale, S.M. / Makde, R.D.
History
DepositionJun 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: 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 E
B: Peptidase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4594
Polymers57,1922
Non-polymers2662
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, protein elutes as single symmetric peak on Superdex 200 column that corresponds to dimeric molecular mass (53,000 Daltons)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-24 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.155, 42.889, 89.290
Angle α, β, γ (deg.)90.00, 107.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidase E / Alpha-aspartyl dipeptidase / Asp-specific dipeptidase / Dipeptidase E


Mass: 28596.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: pepE, STM4190 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36936, dipeptidase E
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
Details: 0.1 M Bis-tris pH 5.5, 0.2 M Sodium chloride, 31 % Peg 3350
PH range: 5.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2018 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.827→45.34 Å / Num. obs: 41754 / % possible obs: 96.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Rrim(I) all: 0.07 / Net I/σ(I): 13.4
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2142 / CC1/2: 0.74 / Rpim(I) all: 0.369 / Rrim(I) all: 0.601 / % possible all: 79.5

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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: 1FY2

1fy2


Resolution: 1.828→41.605 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1
RfactorNum. reflection% reflection
Rfree0.2126 2062 4.94 %
Rwork0.189 --
obs0.1902 41715 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.828→41.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 18 269 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033652
X-RAY DIFFRACTIONf_angle_d0.6434991
X-RAY DIFFRACTIONf_dihedral_angle_d14.4112162
X-RAY DIFFRACTIONf_chiral_restr0.048571
X-RAY DIFFRACTIONf_plane_restr0.005662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8279-1.87040.40641160.32742201X-RAY DIFFRACTION80
1.8704-1.91720.31941660.28492572X-RAY DIFFRACTION96
1.9172-1.9690.26481400.24372620X-RAY DIFFRACTION96
1.969-2.0270.2671360.2142654X-RAY DIFFRACTION96
2.027-2.09240.23591340.21912627X-RAY DIFFRACTION96
2.0924-2.16720.22061630.1872636X-RAY DIFFRACTION97
2.1672-2.25390.26561370.20242603X-RAY DIFFRACTION95
2.2539-2.35650.20061260.18672672X-RAY DIFFRACTION97
2.3565-2.48070.2021480.18172677X-RAY DIFFRACTION97
2.4807-2.63610.21011100.19082684X-RAY DIFFRACTION97
2.6361-2.83960.23361590.1972697X-RAY DIFFRACTION98
2.8396-3.12530.20211310.19672695X-RAY DIFFRACTION98
3.1253-3.57730.20261420.18412720X-RAY DIFFRACTION98
3.5773-4.50620.16511230.15432759X-RAY DIFFRACTION98
4.5062-41.61570.15671310.15572836X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -11.8147 Å / Origin y: -0.4214 Å / Origin z: -21.3299 Å
111213212223313233
T0.1324 Å20.0151 Å2-0.0155 Å2-0.0882 Å2-0.0024 Å2--0.1118 Å2
L1.2597 °20.1006 °2-0.3105 °2-0.2607 °2-0.077 °2--0.5571 °2
S-0.02 Å °0.0211 Å °0.0192 Å °0.0149 Å °0.012 Å °-0.0192 Å °-0.0096 Å °-0.0765 Å °0.0072 Å °
Refinement TLS groupSelection details: all

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