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- PDB-3vh9: Crystal structure of Aeromonas proteolytica aminopeptidase comple... -

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Basic information

Entry
Database: PDB / ID: 3vh9
TitleCrystal structure of Aeromonas proteolytica aminopeptidase complexed with 8-quinolinol
ComponentsBacterial leucyl aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 8-Quinolinol / Dinuclear zinc hydrolases / Aminopeptidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28E, aminopeptidase AP1 / Peptidase M28 family / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
quinolin-8-ol / THIOCYANATE ION / Bacterial leucyl aminopeptidase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsSaijo, S. / Hanaya, K. / Suetsugu, M. / Kobayashi, K. / Yamato, I. / Aoki, S.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2012
Title: Potent inhibition of dinuclear zinc(II) peptidase, an aminopeptidase from Aeromonas proteolytica, by 8-quinolinol derivatives: inhibitor design based on Zn(2+) fluorophores, kinetic, and X-ray ...Title: Potent inhibition of dinuclear zinc(II) peptidase, an aminopeptidase from Aeromonas proteolytica, by 8-quinolinol derivatives: inhibitor design based on Zn(2+) fluorophores, kinetic, and X-ray crystallographic study.
Authors: Hanaya, K. / Suetsugu, M. / Saijo, S. / Yamato, I. / Aoki, S.
History
DepositionAug 24, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_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_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,24825
Polymers32,2381
Non-polymers1,01024
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.463, 108.463, 90.737
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-473-

HOH

21A-542-

HOH

31A-663-

HOH

41A-692-

HOH

51A-719-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacterial leucyl aminopeptidase


Mass: 32238.150 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 107-405 / Source method: isolated from a natural source / Source: (natural) Vibrio proteolyticus (bacteria)
References: UniProt: Q01693, bacterial leucyl aminopeptidase

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Non-polymers , 7 types, 440 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HQY / quinolin-8-ol / 8-hydroxyquinoline


Mass: 145.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-HCl, 100mM KSCN, 4.5M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→15 Å / Num. all: 79057 / Num. obs: 79004 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 21.4 % / Biso Wilson estimate: 9.27 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 65.9
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 21 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 8.6 / Num. unique all: 3901 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PEB ENTRY 1LOK

1lok


Resolution: 1.29→13.618 Å / SU ML: 0.21 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 11.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 3972 5.03 %RANDOM
Rwork0.1313 ---
obs0.1324 79000 99.96 %-
all-79045 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.334 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4582 Å20 Å2-0 Å2
2--0.4582 Å2-0 Å2
3----0.9165 Å2
Refinement stepCycle: LAST / Resolution: 1.29→13.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 43 416 2669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122417
X-RAY DIFFRACTIONf_angle_d1.4513290
X-RAY DIFFRACTIONf_dihedral_angle_d13.058863
X-RAY DIFFRACTIONf_chiral_restr0.092366
X-RAY DIFFRACTIONf_plane_restr0.009427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.2901-1.30580.21141180.160126672667100
1.3058-1.32230.19561530.151326482648100
1.3223-1.33970.18291340.136426232623100
1.3397-1.3580.14951240.121426592659100
1.358-1.37740.14831510.116426152615100
1.3774-1.39790.15591570.115726282628100
1.3979-1.41980.16511250.10726862686100
1.4198-1.4430.13121410.095526492649100
1.443-1.46790.13471610.094626152615100
1.4679-1.49450.12431350.095326342634100
1.4945-1.52320.12451220.096926732673100
1.5232-1.55430.12971390.096626762676100
1.5543-1.5880.12021550.099226252625100
1.588-1.62490.13991450.098626592659100
1.6249-1.66550.15571420.106126642664100
1.6655-1.71040.1421380.111226642664100
1.7104-1.76070.1661370.119126682668100
1.7607-1.81740.12751510.119626602660100
1.8174-1.88220.14941470.123226782678100
1.8822-1.95730.15361260.123926962696100
1.9573-2.04610.15521440.12726902690100
2.0461-2.15360.14541330.127926842684100
2.1536-2.28790.16251460.128527042704100
2.2879-2.46360.1481670.14226992699100
2.4636-2.70980.17511470.156827222722100
2.7098-3.09790.19371400.16927432743100
3.0979-3.88790.1291590.136127722772100
3.8879-13.61840.16841350.15382927292799

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