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

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Basic information

Entry
Database: PDB / ID: 5wdk
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-T1O / Aminopeptidase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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
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
Revision 1.3Oct 9, 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)277,59923
Polymers275,3726
Non-polymers2,22617
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17820 Å2
ΔGint-89 kcal/mol
Surface area79890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.912, 136.969, 208.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aminopeptidase C


Mass: 45895.367 Da / Num. of mol.: 6 / Fragment: UNP residues 23-405
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-T1O / 5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide


Mass: 299.389 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H21N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25 M K/Na tartrate, 17.5% PEG3350, 1 mM ZnCl2

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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: Jan 8, 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: 2.35→50.1 Å / Num. obs: 120727 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.08 Å2 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.06 / Rsym value: 0.14 / Net I/σ(I): 13.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 5972 / CC1/2: 0.744 / Rpim(I) all: 0.4 / Rsym value: 0.96 / Χ2: 0.683 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PW3

3pw3


Resolution: 2.36→50.1 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.26
RfactorNum. reflection% reflection
Rfree0.2311 6066 5.03 %
Rwork0.1862 --
obs0.1885 120638 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.08 Å2 / Biso mean: 60.7596 Å2 / Biso min: 26.9 Å2
Refinement stepCycle: final / Resolution: 2.36→50.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16703 0 131 558 17392
Biso mean--82.41 47.82 -
Num. residues----2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817293
X-RAY DIFFRACTIONf_angle_d0.92423496
X-RAY DIFFRACTIONf_chiral_restr0.0522497
X-RAY DIFFRACTIONf_plane_restr0.0063038
X-RAY DIFFRACTIONf_dihedral_angle_d15.41410035
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 (%)
2.3643-2.39120.31661450.24822790293573
2.3912-2.41930.33272150.246738324047100
2.4193-2.44880.29892220.234137663988100
2.4488-2.47980.31191950.244138204015100
2.4798-2.51250.29291960.240438094005100
2.5125-2.54690.30841990.236238194018100
2.5469-2.58330.28552020.231838074009100
2.5833-2.62180.29131930.216638584051100
2.6218-2.66280.27192000.226238254025100
2.6628-2.70640.32140.221537934007100
2.7064-2.75310.27632010.218538214022100
2.7531-2.80320.25181970.215138204017100
2.8032-2.85710.29642050.21563790399599
2.8571-2.91540.27931940.229338534047100
2.9154-2.97880.29722050.227238424047100
2.9788-3.04810.29712040.226238344038100
3.0481-3.12430.30932070.221238404047100
3.1243-3.20870.27551960.213938194015100
3.2087-3.30310.24492060.209638444050100
3.3031-3.40970.25542040.199238644068100
3.4097-3.53160.23232090.194438364045100
3.5316-3.67290.23451830.183838674050100
3.6729-3.840.20212100.172538694079100
3.84-4.04240.21592180.165438474065100
4.0424-4.29550.1891880.150139114099100
4.2955-4.6270.17622310.140138544085100
4.627-5.09220.19291850.134939354120100
5.0922-5.82810.2012140.158539024116100
5.8281-7.33910.20321880.184940034191100
7.3391-50.13210.17992400.173141024342100
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)
10.2265-0.2198-0.20550.6638-0.09880.3899-0.446-0.3241-0.3460.36550.25170.23280.62350.4725-0.07290.83420.34820.10020.69550.18860.508849.1168-22.0524-6.224
21.6185-0.5436-0.32060.74920.63511.4754-0.1379-0.3311-0.14760.28970.07870.04080.3930.4095-0.00970.50930.10070.01120.50050.06680.352939.8739-3.0911-3.3791
31.4642-0.4972-1.31191.0377-0.24182.5425-0.4126-0.3499-0.36090.04350.23030.10870.80830.4539-0.0080.66820.260.05840.58830.09350.523155.3421-20.1345-19.8293
40.3470.07960.25960.432-0.02610.2052-0.13050.06170.10360.1781-0.06260.1211-0.2404-0.34190.00020.57560.11640.02780.5-0.06930.61282.954127.127-5.2814
50.958-0.7778-0.50751.24120.32251.3759-0.06-0.0021-0.0430.3073-0.10580.20340.0231-0.1136-0.00070.4656-0.00550.08110.4034-0.02220.442712.86178.7183-1.412
60.9534-0.63640.65051.24490.62391.86930.01150.31910.0001-0.1073-0.26880.3324-0.3484-0.3319-0.00020.43360.12230.02070.641-0.13160.682-5.727722.5012-15.6695
70.3379-0.31680.18170.527-0.35120.23410.3582-0.3749-0.13890.3308-0.38030.18830.8318-0.5445-0.04470.8992-0.53060.17671.0293-0.18270.6844-7.2559-26.5662-21.3116
80.73660.08260.19390.60130.34051.54040.1288-0.21150.09340.1808-0.52160.50080.2508-0.7516-0.06710.3847-0.0620.07920.8968-0.30640.697-8.2733-7.8865-31.1873
90.72740.46630.39050.32070.20221.18550.428-0.6115-0.14740.4505-0.49290.1350.9982-0.9813-0.011.0333-0.49640.18530.9425-0.04940.65670.7041-22.5356-9.4273
100.20680.15430.0660.3655-0.12840.1428-0.13930.26790.8406-0.0967-0.03510.3812-0.4867-0.1418-0.13080.86640.1094-0.37750.60410.21560.94117.561523.5604-63.6892
111.70070.5319-0.14831.0467-0.12950.8357-0.18240.10270.3367-0.198-0.02320.4945-0.1687-0.3037-0.01380.46360.1126-0.17960.5367-0.07830.61191.97154.6491-56.2166
122.42740.0936-0.41010.796-0.5650.7783-0.2720.55381.0033-0.35970.17520.3074-0.3613-0.15710.00730.7977-0.0117-0.2710.6150.22850.768922.489121.7636-65.1808
130.7833-0.06710.23530.41940.07990.15220.0573-0.0027-0.1390.2542-0.11780.07050.13250.1077-0.00050.48120.00110.0160.3539-0.03740.451133.4342-27.3615-61.7457
140.45980.00880.16610.97090.93411.2786-0.00640.0399-0.0416-0.1897-0.001-0.0341-0.06560.0319-0.00010.43130.0110.00870.3320.02550.37740.3801-7.3434-58.976
151.7092-0.52240.03451.12450.70990.607-0.0516-0.064-0.31150.119-0.06130.30020.0443-0.19520.00030.4519-0.01340.0160.442-0.04890.494119.4012-24.2603-61.9515
160.30030.1954-0.36290.50440.03980.6375-0.0094-0.03960.0353-0.2102-0.02880.1597-0.0601-0.1159-0.00030.4205-0.0233-0.00510.33710.00390.425254.897529.2646-31.264
170.88420.60050.08971.34740.48070.3982-0.01490.05690.0039-0.1129-0.0023-0.1707-0.0570.081700.37770.01410.01220.33320.02870.364154.8858.9814-38.5051
180.32230.5376-0.12811.2211-0.11751.10680.0237-0.10340.13240.1694-0.01640.1546-0.1323-0.133200.4273-0.01-0.00310.423-0.01440.422747.74628.1299-17.4684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 71 )A33 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 216 )A72 - 216
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 405 )A217 - 405
4X-RAY DIFFRACTION4chain 'B' and (resid 33 through 71 )B33 - 71
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 216 )B72 - 216
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 405 )B217 - 405
7X-RAY DIFFRACTION7chain 'C' and (resid 33 through 71 )C33 - 71
8X-RAY DIFFRACTION8chain 'C' and (resid 72 through 216 )C72 - 216
9X-RAY DIFFRACTION9chain 'C' and (resid 217 through 404 )C217 - 404
10X-RAY DIFFRACTION10chain 'D' and (resid 33 through 71 )D33 - 71
11X-RAY DIFFRACTION11chain 'D' and (resid 72 through 216 )D72 - 216
12X-RAY DIFFRACTION12chain 'D' and (resid 217 through 405 )D217 - 405
13X-RAY DIFFRACTION13chain 'E' and (resid 32 through 71 )E32 - 71
14X-RAY DIFFRACTION14chain 'E' and (resid 72 through 216 )E72 - 216
15X-RAY DIFFRACTION15chain 'E' and (resid 217 through 405 )E217 - 405
16X-RAY DIFFRACTION16chain 'F' and (resid 32 through 71 )F32 - 71
17X-RAY DIFFRACTION17chain 'F' and (resid 72 through 216 )F72 - 216
18X-RAY DIFFRACTION18chain 'F' and (resid 217 through 405 )F217 - 405

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