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- PDB-6w4n: Co-crystal structure of Pd_dinase with probe glycine-propargylgly... -

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Basic information

Entry
Database: PDB / ID: 6w4n
TitleCo-crystal structure of Pd_dinase with probe glycine-propargylglycine-AOMK
ComponentsAminopeptidase
KeywordsHYDROLASE / Diaminopeptidase
Function / homology
Function and homology information


cysteine-type aminopeptidase activity / homocysteine catabolic process / response to toxic substance / proteolysis / cytoplasm
Similarity search - Function
Peptidase C1B, bleomycin hydrolase / Peptidase C1-like family / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / Chem-SWJ / Aminopeptidase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.623 Å
AuthorsXu, J.H. / Solania, A. / Wolan, D.W.
CitationJournal: To Be Published
Title: Co-crystal structure of Pd_dinase with probe glycine-propargylglycine-AOMK
Authors: Xu, J.H. / Solania, A. / Wolan, D.W.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)276,85124
Polymers275,3726
Non-polymers1,47818
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18160 Å2
ΔGint-89 kcal/mol
Surface area78160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.113, 138.613, 220.130
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
13GLYGLYLYSLYS(chain A and (resid 33 through 34 or (resid 35...AA33 - 40529 - 401
14GLYGLYLYSLYS(chain A and (resid 33 through 34 or (resid 35...AA33 - 40529 - 401
15GLYGLYLYSLYS(chain A and (resid 33 through 34 or (resid 35...AA33 - 40529 - 401
16GLYGLYLYSLYS(chain A and (resid 33 through 34 or (resid 35...AA33 - 40529 - 401
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
23GLYGLYLYSLYS(chain B and (resid 33 through 34 or (resid 35...BB33 - 40529 - 401
24GLYGLYLYSLYS(chain B and (resid 33 through 34 or (resid 35...BB33 - 40529 - 401
25GLYGLYLYSLYS(chain B and (resid 33 through 34 or (resid 35...BB33 - 40529 - 401
26GLYGLYLYSLYS(chain B and (resid 33 through 34 or (resid 35...BB33 - 40529 - 401
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
33GLYGLYILEILE(chain C and (resid 33 through 34 or (resid 35...CC33 - 40429 - 400
34GLYGLYILEILE(chain C and (resid 33 through 34 or (resid 35...CC33 - 40429 - 400
35GLYGLYILEILE(chain C and (resid 33 through 34 or (resid 35...CC33 - 40429 - 400
36GLYGLYILEILE(chain C and (resid 33 through 34 or (resid 35...CC33 - 40429 - 400
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
43GLYGLYLYSLYS(chain D and (resid 33 through 159 or (resid 160...DD33 - 40529 - 401
44GLYGLYLYSLYS(chain D and (resid 33 through 159 or (resid 160...DD33 - 40529 - 401
45GLYGLYLYSLYS(chain D and (resid 33 through 159 or (resid 160...DD33 - 40529 - 401
46GLYGLYLYSLYS(chain D and (resid 33 through 159 or (resid 160...DD33 - 40529 - 401
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
53GLYGLYLYSLYS(chain E and (resid 33 through 34 or (resid 35...EE33 - 40529 - 401
54GLYGLYLYSLYS(chain E and (resid 33 through 34 or (resid 35...EE33 - 40529 - 401
55GLYGLYLYSLYS(chain E and (resid 33 through 34 or (resid 35...EE33 - 40529 - 401
56GLYGLYLYSLYS(chain E and (resid 33 through 34 or (resid 35...EE33 - 40529 - 401
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
63GLYGLYLYSLYS(chain F and (resid 33 through 34 or (resid 35...FF33 - 40529 - 401
64GLYGLYLYSLYS(chain F and (resid 33 through 34 or (resid 35...FF33 - 40529 - 401
65GLYGLYLYSLYS(chain F and (resid 33 through 34 or (resid 35...FF33 - 40529 - 401
66GLYGLYLYSLYS(chain F and (resid 33 through 34 or (resid 35...FF33 - 40529 - 401

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Components

#1: Protein
Aminopeptidase


Mass: 45895.367 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria)
Gene: DW188_02780, DW692_01025, DW700_01025, DW808_17970, DW814_08450, DW867_06285, DW984_01045, DW998_13650, DWW19_04025, DWY54_02375, DWZ58_02465, DXD05_07510
Production host: Escherichia coli (E. coli) / References: UniProt: A0A395YY96
#2: Chemical
ChemComp-SWJ / 2-azanyl-~{N}-[(3~{S})-2-oxidanylidenehex-5-yn-3-yl]ethanamide


Mass: 168.193 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H12N2O2 / 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.: 561 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M K/Na Tartrate, 15% PEG3350, 1 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 96251 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 39.96 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.048 / Rrim(I) all: 0.133 / Χ2: 0.906 / Net I/σ(I): 5.5 / Num. measured all: 707012
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.677.50.76447280.7240.2930.820.93399.6
2.67-2.717.50.66747730.7890.2550.7150.9199.9
2.71-2.777.50.56947820.8390.2190.6110.91599.9
2.77-2.827.50.52847710.8620.2030.5660.90999.9
2.82-2.887.40.45147790.90.1740.4840.9199.9
2.88-2.957.30.3948020.9270.1520.4190.89499.8
2.95-3.027.10.34847580.9350.1380.3750.9199.7
3.02-3.116.70.27247120.9510.1110.2950.9197.9
3.11-3.27.70.24247980.970.0920.260.9299.9
3.2-3.37.60.19148060.9820.0730.2050.93299.9
3.3-3.427.60.15747920.9870.060.1690.91999.8
3.42-3.567.30.12848320.9910.050.1380.93999.8
3.56-3.727.10.1147920.9920.0440.1190.95199.9
3.72-3.9170.09147520.9940.0360.0980.94998.1
3.91-4.167.60.07848450.9960.030.0840.94699.6
4.16-4.487.50.06848570.9970.0260.0730.95299.8
4.48-4.937.10.0648350.9970.0240.0640.94299.1
4.93-5.647.50.06148290.9970.0240.0660.96398.4
5.64-7.117.30.06249560.9970.0240.0670.9899.9
7.11-5070.0450520.9990.0160.0430.42997.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pw3

3pw3


Resolution: 2.623→49.143 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 4831 5.02 %
Rwork0.2075 91316 -
obs0.2086 96147 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.37 Å2 / Biso mean: 47.4049 Å2 / Biso min: 14.54 Å2
Refinement stepCycle: final / Resolution: 2.623→49.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16733 0 84 561 17378
Biso mean--53.53 37.94 -
Num. residues----2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517272
X-RAY DIFFRACTIONf_angle_d0.823423
X-RAY DIFFRACTIONf_chiral_restr0.0462468
X-RAY DIFFRACTIONf_plane_restr0.0043026
X-RAY DIFFRACTIONf_dihedral_angle_d5.16511328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9585X-RAY DIFFRACTION11.179TORSIONAL
12B9585X-RAY DIFFRACTION11.179TORSIONAL
13C9585X-RAY DIFFRACTION11.179TORSIONAL
14D9585X-RAY DIFFRACTION11.179TORSIONAL
15E9585X-RAY DIFFRACTION11.179TORSIONAL
16F9585X-RAY DIFFRACTION11.179TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6233-2.65310.32781420.2845294998
2.6531-2.68430.33611420.2692300399
2.6843-2.71710.30631600.26613040100
2.7171-2.75140.29071670.25843020100
2.7514-2.78760.30191470.25383024100
2.7876-2.82580.26441610.25063035100
2.8258-2.86620.29091550.25383036100
2.8662-2.9090.28651650.25593020100
2.909-2.95440.2691410.25633076100
2.9544-3.00290.26821620.26473030100
3.0029-3.05460.33781900.2628294798
3.0546-3.11020.25541670.2537296898
3.1102-3.170.26221740.24023038100
3.17-3.23470.25721860.24043003100
3.2347-3.3050.2681640.23213050100
3.305-3.38180.25881390.22663080100
3.3818-3.46640.24831580.22813024100
3.4664-3.56010.24461640.21563061100
3.5601-3.66480.21591550.20523054100
3.6648-3.78310.20151600.1857297997
3.7831-3.91820.20931820.18353011100
3.9182-4.0750.19581690.18483071100
4.075-4.26040.19371510.16663068100
4.2604-4.48490.19451530.16813088100
4.4849-4.76560.18391650.16173088100
4.7656-5.13320.19681520.1639300397
5.1332-5.64910.19281740.17583080100
5.6491-6.4650.22221710.19883128100
6.465-8.13930.17941530.1937310898
8.1393-49.1430.19281620.1899323498

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