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- PDB-5wze: The structure of Pseudomonas aeruginosa aminopeptidase PepP -

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Basic information

Entry
Database: PDB / ID: 5wze
TitleThe structure of Pseudomonas aeruginosa aminopeptidase PepP
ComponentsAminopeptidase P
KeywordsHYDROLASE / aminopeptidase / Pseudomonas aeruginosa / pathogenicity
Function / homology
Function and homology information


metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / proteolysis / cytosol
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE / : / TRIETHYLENE GLYCOL / PROLINE / Aminopeptidase P
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.783 Å
AuthorsBao, R. / Peng, C.T. / Liu, L. / He, L.H. / Li, C.C. / Li, T. / Shen, Y.L. / Zhu, Y.B. / Song, Y.J.
CitationJournal: Front Microbiol / Year: 2017
Title: Structure-Function Relationship of Aminopeptidase P from Pseudomonas aeruginosa.
Authors: Peng, C.T. / Liu, L. / Li, C.C. / He, L.H. / Li, T. / Shen, Y.L. / Gao, C. / Wang, N.Y. / Xia, Y. / Zhu, Y.B. / Song, Y.J. / Lei, Q. / Yu, L.T. / Bao, R.
History
DepositionJan 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_asym_id / _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_asym_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_asym_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 / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase P
B: Aminopeptidase P
C: Aminopeptidase P
D: Aminopeptidase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,09044
Polymers203,3824
Non-polymers2,70740
Water20,7531152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-189 kcal/mol
Surface area72040 Å2
Unit cell
Length a, b, c (Å)111.197, 123.432, 149.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aminopeptidase P


Mass: 50845.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: pepP, PA5224
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9HTW6

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Non-polymers , 10 types, 1192 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1152 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG400, 100 mM sodium cacodylate pH 6.5, 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.783→48.01 Å / Num. obs: 194517 / % possible obs: 99 % / Redundancy: 8.9 % / Net I/σ(I): 19.714
Reflection shellResolution: 1.783→1.8275 Å / Rmerge(I) obs: 0.709 / Num. unique obs: 18600

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZ9

1az9
PDB Unreleased entry


Resolution: 1.783→48.008 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 2000 1.03 %
Rwork0.2105 --
obs0.2106 194405 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.783→48.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13997 0 133 1153 15283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114524
X-RAY DIFFRACTIONf_angle_d0.99719684
X-RAY DIFFRACTIONf_dihedral_angle_d23.415441
X-RAY DIFFRACTIONf_chiral_restr0.0732082
X-RAY DIFFRACTIONf_plane_restr0.0062611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7829-1.82750.38261340.382112907X-RAY DIFFRACTION94
1.8275-1.8770.37581420.366413617X-RAY DIFFRACTION100
1.877-1.93220.35481420.339913666X-RAY DIFFRACTION100
1.9322-1.99460.34171420.317313680X-RAY DIFFRACTION100
1.9946-2.06580.29761420.2913639X-RAY DIFFRACTION100
2.0658-2.14860.29081430.258213720X-RAY DIFFRACTION100
2.1486-2.24630.25171420.232713725X-RAY DIFFRACTION100
2.2463-2.36480.26431430.217613758X-RAY DIFFRACTION100
2.3648-2.51290.21941430.211813780X-RAY DIFFRACTION100
2.5129-2.70690.25381440.213513798X-RAY DIFFRACTION100
2.7069-2.97930.21791440.209113849X-RAY DIFFRACTION100
2.9793-3.41030.24621440.202713868X-RAY DIFFRACTION100
3.4103-4.29620.16441460.160814016X-RAY DIFFRACTION100
4.2962-48.02520.13521490.14914382X-RAY DIFFRACTION100

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