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- PDB-6a4s: Crystal structure of peptidase E with ordered active site loop fr... -

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Basic information

Entry
Database: PDB / ID: 6a4s
TitleCrystal structure of peptidase E with ordered active site loop from Salmonella enterica
ComponentsPeptidase EDipeptidase E
KeywordsHYDROLASE / S51 peptidase / peptidase E / dimer / 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
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 31, 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


Theoretical massNumber of molelcules
Total (without water)57,1922
Polymers57,1922
Non-polymers00
Water5,531307
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 area3330 Å2
ΔGint-24 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.452, 42.933, 89.149
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidase E / Dipeptidase 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 6.5
Details: 0.1 M Bis-tris pH6.5, 0.2 M Sodium Chloride, 25 % PEG 3350
PH range: 5-6.5

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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 6, 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: 1.9→45.77 Å / Num. obs: 38789 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2495 / CC1/2: 0.886 / Rpim(I) all: 0.254 / Rrim(I) all: 0.465 / % possible all: 99.3

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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: 1.9→41.461 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.211 1887 4.87 %
Rwork0.182 --
obs0.1834 38756 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 0 310 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073610
X-RAY DIFFRACTIONf_angle_d0.8744931
X-RAY DIFFRACTIONf_dihedral_angle_d13.7792134
X-RAY DIFFRACTIONf_chiral_restr0.056566
X-RAY DIFFRACTIONf_plane_restr0.006650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.30841510.25812832X-RAY DIFFRACTION99
1.9514-2.00880.25931540.23582770X-RAY DIFFRACTION99
2.0088-2.07360.26591400.20892815X-RAY DIFFRACTION99
2.0736-2.14780.21941590.20022833X-RAY DIFFRACTION99
2.1478-2.23370.24391550.20532791X-RAY DIFFRACTION99
2.2337-2.33540.231430.19282819X-RAY DIFFRACTION99
2.3354-2.45850.23481410.18072809X-RAY DIFFRACTION99
2.4585-2.61250.23961340.19252860X-RAY DIFFRACTION99
2.6125-2.81420.23691620.19022814X-RAY DIFFRACTION99
2.8142-3.09730.221330.1932873X-RAY DIFFRACTION100
3.0973-3.54530.17411500.18152852X-RAY DIFFRACTION100
3.5453-4.46590.17821290.15012883X-RAY DIFFRACTION99
4.4659-41.47050.16521360.15082918X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -12.3172 Å / Origin y: -0.4181 Å / Origin z: -21.272 Å
111213212223313233
T0.1262 Å20.011 Å2-0.017 Å2-0.0836 Å2-0.0034 Å2--0.1121 Å2
L1.4367 °20.1412 °2-0.423 °2-0.2275 °2-0.1092 °2--0.5917 °2
S-0.0085 Å °0.028 Å °0.012 Å °0.0077 Å °0.0062 Å °-0.0152 Å °-0.0125 Å °-0.0802 Å °0.0048 Å °
Refinement TLS groupSelection details: all

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