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- PDB-5wdl: A processive dipeptidyl aminopeptidase secreted from an establish... -

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Basic information

Entry
Database: PDB / ID: 5wdl
TitleA processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis
ComponentsAminopeptidase C
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


cysteine-type aminopeptidase activity / homocysteine catabolic process / response to toxic substance / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Peptidase C1B, bleomycin hydrolase / Peptidase C1-like family / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Chem-R33 / Aminopeptidase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.625 Å
AuthorsWolan, D.W. / Xu, J.H. / Solania, A. / Chatterjee, S. / Jiang, Z. / ODonoghue, A.J.
CitationJournal: Acs Chem.Biol. / Year: 2018
Title: A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.
Authors: Xu, J.H. / Jiang, Z. / Solania, A. / Chatterjee, S. / Suzuki, B. / Lietz, C.B. / Hook, V.Y.H. / O'Donoghue, A.J. / Wolan, D.W.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase C
B: Aminopeptidase C
C: Aminopeptidase C
D: Aminopeptidase C
E: Aminopeptidase C
F: Aminopeptidase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,21724
Polymers275,3726
Non-polymers1,84518
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18390 Å2
ΔGint-94 kcal/mol
Surface area84050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.841, 140.299, 221.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 33 through 34 or (resid 35...
21(chain B and (resid 33 through 34 or (resid 35...
31(chain C and (resid 33 through 34 or (resid 35...
41(chain D and (resid 33 through 159 or (resid 160...
51(chain E and (resid 33 through 34 or (resid 35...
61(chain F and (resid 33 through 34 or (resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPHEPHE(chain A and (resid 33 through 34 or (resid 35...AA33 - 3429 - 30
12VALVALVALVAL(chain A and (resid 33 through 34 or (resid 35...AA3531
13GLYGLYR33R33(chain A and (resid 33 through 34 or (resid 35...AA - G33 - 50129
14GLYGLYR33R33(chain A and (resid 33 through 34 or (resid 35...AA - G33 - 50129
15GLYGLYR33R33(chain A and (resid 33 through 34 or (resid 35...AA - G33 - 50129
16GLYGLYR33R33(chain A and (resid 33 through 34 or (resid 35...AA - G33 - 50129
21GLYGLYPHEPHE(chain B and (resid 33 through 34 or (resid 35...BB33 - 3429 - 30
22VALVALVALVAL(chain B and (resid 33 through 34 or (resid 35...BB3531
23GLYGLYR33R33(chain B and (resid 33 through 34 or (resid 35...BB - J33 - 50129
24GLYGLYR33R33(chain B and (resid 33 through 34 or (resid 35...BB - J33 - 50129
25GLYGLYR33R33(chain B and (resid 33 through 34 or (resid 35...BB - J33 - 50129
26GLYGLYR33R33(chain B and (resid 33 through 34 or (resid 35...BB - J33 - 50129
31GLYGLYPHEPHE(chain C and (resid 33 through 34 or (resid 35...CC33 - 3429 - 30
32VALVALVALVAL(chain C and (resid 33 through 34 or (resid 35...CC3531
33GLYGLYR33R33(chain C and (resid 33 through 34 or (resid 35...CC - M33 - 50129
34GLYGLYR33R33(chain C and (resid 33 through 34 or (resid 35...CC - M33 - 50129
35GLYGLYR33R33(chain C and (resid 33 through 34 or (resid 35...CC - M33 - 50129
36GLYGLYR33R33(chain C and (resid 33 through 34 or (resid 35...CC - M33 - 50129
41GLYGLYGLYGLY(chain D and (resid 33 through 159 or (resid 160...DD33 - 15929 - 155
42LYSLYSLYSLYS(chain D and (resid 33 through 159 or (resid 160...DD160156
43GLYGLYR33R33(chain D and (resid 33 through 159 or (resid 160...DD - P33 - 50129
44GLYGLYR33R33(chain D and (resid 33 through 159 or (resid 160...DD - P33 - 50129
45GLYGLYR33R33(chain D and (resid 33 through 159 or (resid 160...DD - P33 - 50129
46GLYGLYR33R33(chain D and (resid 33 through 159 or (resid 160...DD - P33 - 50129
51GLYGLYPHEPHE(chain E and (resid 33 through 34 or (resid 35...EE33 - 3429 - 30
52VALVALVALVAL(chain E and (resid 33 through 34 or (resid 35...EE3531
53GLYGLYR33R33(chain E and (resid 33 through 34 or (resid 35...EE - S33 - 50129
54GLYGLYR33R33(chain E and (resid 33 through 34 or (resid 35...EE - S33 - 50129
55GLYGLYR33R33(chain E and (resid 33 through 34 or (resid 35...EE - S33 - 50129
56GLYGLYR33R33(chain E and (resid 33 through 34 or (resid 35...EE - S33 - 50129
61GLYGLYPHEPHE(chain F and (resid 33 through 34 or (resid 35...FF33 - 3429 - 30
62VALVALVALVAL(chain F and (resid 33 through 34 or (resid 35...FF3531
63GLYGLYR33R33(chain F and (resid 33 through 34 or (resid 35...FF - V33 - 50129
64GLYGLYR33R33(chain F and (resid 33 through 34 or (resid 35...FF - V33 - 50129
65GLYGLYR33R33(chain F and (resid 33 through 34 or (resid 35...FF - V33 - 50129
66GLYGLYR33R33(chain F and (resid 33 through 34 or (resid 35...FF - V33 - 50129

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Components

#1: Protein
Aminopeptidase C


Mass: 45895.367 Da / Num. of mol.: 6 / Fragment: UNP residues 33-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152) (bacteria)
Strain: ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152
Gene: BDI_2249
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A6LE66
#2: Chemical
ChemComp-R33 / N-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]glycinamide


Mass: 229.279 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C9H19N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.27 M K/Na Tartrate, 22% PEG3350, 1 mM ZnCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 96577 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.071 / Rsym value: 0.161 / Net I/av σ(I): 12.6 / Net I/σ(I): 12.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.721 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4696 / CC1/2: 0.564 / Rpim(I) all: 0.498 / Rsym value: 1.068 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PW3

3pw3


Resolution: 2.625→49.105 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 4868 5.04 %
Rwork0.1708 91627 -
obs0.1729 96495 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.63 Å2 / Biso mean: 39.3289 Å2 / Biso min: 8.39 Å2
Refinement stepCycle: final / Resolution: 2.625→49.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17387 0 108 780 18275
Biso mean--44.92 33.71 -
Num. residues----2226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217958
X-RAY DIFFRACTIONf_angle_d0.47924373
X-RAY DIFFRACTIONf_chiral_restr0.0392575
X-RAY DIFFRACTIONf_plane_restr0.0033156
X-RAY DIFFRACTIONf_dihedral_angle_d9.47110469
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9979X-RAY DIFFRACTION5.016TORSIONAL
12B9979X-RAY DIFFRACTION5.016TORSIONAL
13C9979X-RAY DIFFRACTION5.016TORSIONAL
14D9979X-RAY DIFFRACTION5.016TORSIONAL
15E9979X-RAY DIFFRACTION5.016TORSIONAL
16F9979X-RAY DIFFRACTION5.016TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6252-2.6550.31611070.26271957206464
2.655-2.68630.28631750.24843039321499
2.6863-2.7190.29041590.23932992315199
2.719-2.75340.28581640.23183070323499
2.7534-2.78970.28031740.22673022319699
2.7897-2.82790.30551560.222730903246100
2.8279-2.86830.25071810.217930403221100
2.8683-2.91110.28431440.222430933237100
2.9111-2.95660.30271580.215730303188100
2.9566-3.0050.28261540.217931073261100
3.005-3.05680.25511740.218730443218100
3.0568-3.11240.26511690.21463067323699
3.1124-3.17230.26871720.20983038321099
3.1723-3.2370.21271490.20113075322499
3.237-3.30740.23071660.185230653231100
3.3074-3.38430.24731390.184931073246100
3.3843-3.46890.23241570.178330833240100
3.4689-3.56270.22351610.168530863247100
3.5627-3.66750.2191730.165730843257100
3.6675-3.78580.19981680.153130723240100
3.7858-3.92110.18481490.15431293278100
3.9211-4.0780.20641710.146430943265100
4.078-4.26350.15251610.133431193280100
4.2635-4.48810.16061680.127631193287100
4.4881-4.76910.14331620.12363094325699
4.7691-5.13690.15481700.127231143284100
5.1369-5.65320.19331630.138831583321100
5.6532-6.46970.20021730.156731413314100
6.4697-8.14510.18121760.159431953371100
8.1451-49.11340.16451750.14873303347899

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