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- PDB-5mfs: The crystal structure of E. coli Aminopeptidase N in complex with... -

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Basic information

Entry
Database: PDB / ID: 5mfs
TitleThe crystal structure of E. coli Aminopeptidase N in complex with 7-amino-4-phenyl-5,7,8,9-tetrahydrobenzocyclohepten-6-one
ComponentsAminopeptidase N
KeywordsHYDROLASE / M1 Aminopeptidase
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold ...Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-7ML / MALONATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsPeng, G. / Olieric, V. / McEwen, A.G. / Schmitt, C. / Albrecht, S. / Cavarelli, J. / Tarnus, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BS07-0020-01 MAMMAMIA France
French National Research AgencyANR-10-INSB-05-01 FRISBI France
CitationJournal: Proteins / Year: 2017
Title: Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis.
Authors: Peng, G. / McEwen, A.G. / Olieric, V. / Schmitt, C. / Albrecht, S. / Cavarelli, J. / Tarnus, C.
History
DepositionNov 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,31640
Polymers101,4411
Non-polymers2,87539
Water31,7601763
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-97 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.827, 120.827, 170.628
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2139-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminopeptidase N / Alpha-aminoacylpeptide hydrolase


Mass: 101441.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pepN, b0932, JW0915 / Production host: Escherichia coli / Strain (production host): BL21(DE3) / References: UniProt: P04825, membrane alanyl aminopeptidase

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Non-polymers , 8 types, 1802 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-7ML / [(7~{S})-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium


Mass: 270.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20NO2
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1763 / 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: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.M M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→89.201 Å / Num. obs: 200123 / % possible obs: 99.9 % / Redundancy: 21.4 % / Biso Wilson estimate: 15.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.187 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.57-1.613.32.9690.335198.3
8.6-89.2200.031199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B34

3b34


Resolution: 1.57→89.201 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.21 / Phase error: 15.61
RfactorNum. reflection% reflection
Rfree0.1388 3398 0.87 %
Rwork0.1134 --
obs0.1137 200028 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.24 Å2 / Biso mean: 23.3578 Å2 / Biso min: 9.14 Å2
Refinement stepCycle: final / Resolution: 1.57→89.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 344 1793 9088
Biso mean--50.32 43.52 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128160
X-RAY DIFFRACTIONf_angle_d1.13711189
X-RAY DIFFRACTIONf_chiral_restr0.0621205
X-RAY DIFFRACTIONf_plane_restr0.0081511
X-RAY DIFFRACTIONf_dihedral_angle_d13.8465148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.59240.34161440.3183156311577598
1.5924-1.61620.34831390.3044159721611199
1.6162-1.64150.30721370.29251607116208100
1.6415-1.66840.29471440.27371609116235100
1.6684-1.69710.33441360.24231609416230100
1.6971-1.7280.23181400.21721615016290100
1.728-1.76120.20661490.19881599216141100
1.7612-1.79720.22751440.18321608616230100
1.7972-1.83630.20661340.16831612916263100
1.8363-1.8790.2061440.15811599516139100
1.879-1.9260.19591420.1471609416236100
1.926-1.97810.15721460.13461609116237100
1.9781-2.03630.14021440.11351606416208100
2.0363-2.1020.13031320.0931602816160100
2.102-2.17710.12361340.08321614816282100
2.1771-2.26430.09251500.07441603716187100
2.2643-2.36740.1121460.07411615516301100
2.3674-2.49220.1211420.07311596916111100
2.4922-2.64840.11781380.07481617516313100
2.6484-2.85290.11031480.07411603916187100
2.8529-3.140.09031380.07431605816196100
3.14-3.59430.09091420.07421609716239100
3.5943-4.52850.09121410.07541604416185100
4.5285-89.34570.13411440.13011607616220100

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