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- PDB-7c9b: Crystal structure of dipeptidase-E from Xenopus laevis -

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Entry
Database: PDB / ID: 7c9b
TitleCrystal structure of dipeptidase-E from Xenopus laevis
ComponentsAlpha-aspartyl dipeptidase
KeywordsHYDROLASE / Peptidase-E / Aspartyl dipeptidase / Alpha-aspartyl dipeptidase
Function / homologydipeptidase E / Peptidase S51 / Peptidase family S51 / dipeptidase activity / Class I glutamine amidotransferase-like / serine-type peptidase activity / proteolysis / cytoplasm / Alpha-aspartyl dipeptidase
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionJun 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / database_2 / entity / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conn / struct_sheet_range / struct_site / struct_site_gen
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_number_measured_all / _reflns.pdbx_redundancy / _reflns.pdbx_scaling_rejects / _reflns.percent_possible_obs / _software.version / _struct.title / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: Rerefined the structure to further account difference map peaks in electron density.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 8, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Feb 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 2.3Nov 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

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Assembly

Deposited unit
A: Alpha-aspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1005
Polymers26,9911
Non-polymers1094
Water3,549197
1
A: Alpha-aspartyl dipeptidase
hetero molecules

A: Alpha-aspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,20010
Polymers53,9822
Non-polymers2188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3100 Å2
ΔGint-62 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.775, 40.900, 74.221
Angle α, β, γ (deg.)90.000, 116.196, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.95 %
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: X-ray mirror, monochromator
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.28→41.5 Å / Num. obs: 49297 / % possible obs: 85.6 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.036 / Rrim(I) all: 0.076 / Net I/σ(I): 10.7 / Num. measured all: 185643 / Scaling rejects: 7
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
1.28-1.311.20.4688647030.750.4640.6590.925.1
7.03-41.54.10.05715583800.9930.0320.06523.598.7

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4S

6a4s


Resolution: 1.4→34.84 Å / SU ML: 0.1499 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 2165 5.04 %
Rwork0.191 40771 -
obs0.1926 42936 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.89 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 4 197 2032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411914
X-RAY DIFFRACTIONf_angle_d1.34162601
X-RAY DIFFRACTIONf_chiral_restr0.1162287
X-RAY DIFFRACTIONf_plane_restr0.0131343
X-RAY DIFFRACTIONf_dihedral_angle_d6.0801262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.325980.27522132X-RAY DIFFRACTION76.16
1.43-1.470.28831340.26152529X-RAY DIFFRACTION90.42
1.47-1.510.29811560.2442721X-RAY DIFFRACTION96.64
1.51-1.550.21611530.2362711X-RAY DIFFRACTION96.69
1.55-1.60.30341450.22352733X-RAY DIFFRACTION97.36
1.6-1.660.24491420.21272713X-RAY DIFFRACTION97.17
1.66-1.730.27251610.22692786X-RAY DIFFRACTION97.71
1.73-1.80.26421580.21872701X-RAY DIFFRACTION97.91
1.8-1.90.26171520.21722761X-RAY DIFFRACTION98.08
1.9-2.020.24231270.20772812X-RAY DIFFRACTION98.49
2.02-2.170.24381510.1962779X-RAY DIFFRACTION98.65
2.18-2.390.19761670.18782796X-RAY DIFFRACTION98.93
2.39-2.740.24591280.19372843X-RAY DIFFRACTION99.2
2.74-3.450.22371390.18572833X-RAY DIFFRACTION99.33
3.45-34.840.16911540.15552921X-RAY DIFFRACTION99.42
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)
12.15578279988-0.14964020510.8757287643151.446073674150.1519091046141.9871465194-0.126997224942-0.09158321221820.07276131147430.179749359017-0.03297228355720.0431216465436-0.522887109642-0.1518768947520.0149006004920.3119962851780.0088609005857-0.1287654573450.191829346047-0.007435138811110.1497840258211.96323710953-3.9477575179922.4522757254
20.4721338556680.008836419864670.06138623984840.4811540356390.561027817991.3644384237-0.1915155745420.01179627397640.2671467244810.179289694695-0.0619249958423-0.178309930468-0.498000349170.418513285861-0.08794410335450.343377074735-0.0565379850845-0.174461347570.3086770256840.05010260099920.23785657112412.9766121763-3.9301525447122.647291937
30.686454027168-0.007627733202-0.01030465124620.6299075107850.1713526038811.26549390514-0.03764620588570.00151902891842-0.045385753890.0960569367063-0.0334644546192-0.06838680283280.05699730365530.2135563323110.02279168013730.1445919394960.00643425100618-0.07067742986950.190577167030.01606749432150.1192170713436.68621312008-13.938135680315.3270041114
42.07402576672-0.242802311761.162115974051.67329079372-1.506257820033.21762941241-0.07207014559690.1692630460850.215776975599-0.156430016925-0.04769248181510.119408878319-0.521185366602-0.2258951413130.07826486345860.2749946573120.0723159706669-0.09799780870490.283699043429-0.01229584271750.139224413097-5.55735175424-3.5124798515910.5445583862
51.63107913240.03922503827611.9747097010.868938350934-0.3449742165436.11250718134-0.1133390664040.03675800681240.08627475925090.0527429968340.005797922360390.00158675142317-0.429935731873-0.3822371910060.1204907554330.2214939435240.143963392811-0.08744594358040.380635747009-0.03890750485680.182556237929-9.22150805371-3.4599487230712.6345652582
60.301042322362-0.07991695284430.541946985050.385049197049-0.5649907310061.45855051452-0.04158142274510.01041186655720.0951372732793-0.0264947542590.06652459671940.0213670455741-0.310904631624-0.2717614302470.3224937197160.4007270018730.369314723285-0.1916904122580.669624593665-0.1331402195810.165180703442-13.56625929480.88274842480316.9764027063
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 22 )1 - 221 - 22
22chain 'A' and (resid 23 through 64 )23 - 6423 - 64
33chain 'A' and (resid 65 through 151 )65 - 15165 - 151
44chain 'A' and (resid 152 through 176 )152 - 176152 - 169
55chain 'A' and (resid 177 through 213 )177 - 213170 - 206
66chain 'A' and (resid 214 through 240 )214 - 240207 - 233

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