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- PDB-7ffp: Crystal structure of di-peptidase-E from Xenopus laevis -

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Basic information

Entry
Database: PDB / ID: 7ffp
TitleCrystal structure of di-peptidase-E from Xenopus laevis
ComponentsAlpha-aspartyl dipeptidase
KeywordsHYDROLASE / Peptidase-E / Aspartyl dipeptidase / Alpha-aspartyl dipeptidase
Function / homology
Function and homology information


dipeptidase E / dipeptidase activity / serine-type peptidase activity / proteolysis / cytoplasm
Similarity search - Function
Peptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
ASPARTIC ACID / Alpha-aspartyl dipeptidase
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKumar, A. / Singh, R. / Makde, R.D.
CitationJournal: Proteins / Year: 2022
Title: Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly.
Authors: Kumar, A. / Singh, R. / Ghosh, B. / Makde, R.D.
History
DepositionJul 23, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 8, 2021ID: 7C9D
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-aspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1643
Polymers26,9911
Non-polymers1732
Water3,441191
1
A: Alpha-aspartyl dipeptidase
hetero molecules

A: Alpha-aspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3286
Polymers53,9822
Non-polymers3464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3790 Å2
ΔGint-40 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.666, 42.150, 75.680
Angle α, β, γ (deg.)90.000, 118.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

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Components

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


Mass: 26990.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: aad-a / Plasmid: pST50Tr / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q91642, dipeptidase E
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 42.84 % / Mosaicity: 0.25 °
Crystal growTemperature: 294 K / Method: microbatch / pH: 7
Details: 50 mM Bis-Tris, 200 mM NaNO3, 10 mM CaCl2, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 7, 2019 / 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: 1.8→41.19 Å / Num. obs: 20727 / % possible obs: 96.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.017 / Rrim(I) all: 0.032 / Net I/σ(I): 29.1 / Num. measured all: 66076 / Scaling rejects: 55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.842.10.0719049020.9910.0540.0899.371.7
9-41.193.30.0266141880.9960.0180.03249.796.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4S

6a4s


Resolution: 1.8→29.22 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1045 5.04 %
Rwork0.1866 19676 -
obs0.1884 20721 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.86 Å2 / Biso mean: 25.0644 Å2 / Biso min: 7.76 Å2
Refinement stepCycle: final / Resolution: 1.8→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 10 200 2094
Biso mean--19.32 37.71 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.890.26261280.22612219234778
1.89-2.010.22491620.21982830299298
2.01-2.170.26631420.21728963038100
2.17-2.390.27011440.19428853029100
2.39-2.730.21981570.193929413098100
2.73-3.440.22091430.187929303073100
3.44-29.220.19011690.15792975314499
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)
10.0774-0.01720.02880.0098-0.00220.0154-0.0923-0.14040.0360.044-0.0016-0.0154-0.0881-0.0802-0.00850.2210.0438-0.01880.1368-0.01060.132.1051-3.404222.3669
20.03040.0216-0.01080.0383-0.03350.0701-0.0643-0.06450.09950.157-0.0114-0.0741-0.16410.0246-0.06680.20880.084-0.04010.1853-0.05840.158410.6215-3.693523.7303
30.00170.00120.00050.0062-0.00640.0151-0.05330.04710.03710.1019-0.0393-0.0951-0.08170.064-0.00050.16270.0016-0.04570.2441-0.02710.246618.7589-3.292519.4579
40.01130.0004-0.01480.00220.0050.0379-0.00070.0115-0.0283-0.0099-0.0199-0.0070.07770.065-0.0710.22870.1844-0.08850.2162-0.06370.170316.3227-16.126321.9516
50.27150.02020.13820.26630.17860.22110.061-0.0648-0.1480.16360.0809-0.01850.21830.07660.18710.14040.04130.00960.0911-0.0030.14275.5556-13.779717.0484
60.03930.01270.05410.05790.11440.211-0.0464-0.03850.0573-0.05680.01630.0786-0.2176-0.2626-0.08940.13890.05750.00550.1251-0.00310.1422-4.6598-3.97335.1229
70.0231-0.0066-0.02060.0050.00690.0167-0.059-0.10880.01460.06170.06050.0103-0.0296-0.11610.06350.19440.13110.00480.2942-0.02810.1333-7.2528-3.02917.9024
80.0261-0.0028-0.01910.03970.01510.0169-0.0501-0.02460.01360.0255-0.00610.0111-0.0618-0.0878-0.10920.2370.42320.0280.5861-0.16030.2-12.90261.580816.8188
97.12663.187.76374.91093.96588.53570.0296-0.13040.0051-0.0034-0.0176-0.01510.0046-0.0254-0.01580.16750.0156-0.01010.1093-0.00640.15994.2106-2.35788.3576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A1 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 49 )A23 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 64 )A50 - 64
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 83 )A65 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 131 )A84 - 131
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 186 )A132 - 186
7X-RAY DIFFRACTION7chain 'A' and (resid 187 through 213 )A187 - 213
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 240 )A214 - 240

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