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

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Basic information

Entry
Database: PDB / ID: 5mft
TitleThe crystal structure of E. coli Aminopeptidase N in complex with 7-amino-1-bromo-4-phenyl-5,7,8,9-tetrahydrobenzocyclohepten-6-one
ComponentsAminopeptidase N
KeywordsHYDROLASE / M1 Aminopeptidase
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta 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 ...Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta 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-7MF / MALONATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 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 2.0Jan 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / 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: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)103,46826
Polymers101,4411
Non-polymers2,02725
Water33,7781875
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-49 kcal/mol
Surface area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.651, 120.651, 170.676
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-2308-

HOH

21A-2317-

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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04825, membrane alanyl aminopeptidase

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Non-polymers , 8 types, 1900 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 349.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19BrNO2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1875 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.8M 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: 1.59→89.11 Å / Num. obs: 192106 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 15.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.59-1.627.51.8950.316197.6
8.71-89.11100.0231199.9

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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: 1.59→60.325 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 15.23
RfactorNum. reflection% reflection
Rfree0.139 3253 0.87 %
Rwork0.111 --
obs0.1112 192025 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.57 Å2 / Biso mean: 22.766 Å2 / Biso min: 8.11 Å2
Refinement stepCycle: final / Resolution: 1.59→60.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 240 1925 9120
Biso mean--47.28 43.13 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128288
X-RAY DIFFRACTIONf_angle_d1.12111391
X-RAY DIFFRACTIONf_chiral_restr0.0611229
X-RAY DIFFRACTIONf_plane_restr0.0081545
X-RAY DIFFRACTIONf_dihedral_angle_d14.4345286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.61380.34711290.3094150731520294
1.6138-1.6390.28841390.2912158451598499
1.639-1.66580.30361440.26921615916303100
1.6658-1.69460.28691400.24231603416174100
1.6946-1.72540.29271360.22641617316309100
1.7254-1.75860.22441490.20351613316282100
1.7586-1.79450.21971440.18961607416218100
1.7945-1.83350.21741300.17381614516275100
1.8335-1.87610.22931500.15861605916209100
1.8761-1.92310.19371440.15231616816312100
1.9231-1.97510.16611460.13891607316219100
1.9751-2.03320.16681420.11851614216284100
2.0332-2.09880.1321360.09721600216138100
2.0988-2.17380.12111340.08611617516309100
2.1738-2.26090.12751500.07731612916279100
2.2609-2.36380.09671420.07291610716249100
2.3638-2.48840.10281420.07021605716199100
2.4884-2.64430.11731380.07021615316291100
2.6443-2.84850.09381520.07311601716169100
2.8485-3.13510.1041380.07441614016278100
3.1351-3.58870.08451430.07241610416247100
3.5887-4.52120.09051390.07371613416273100
4.5212-60.36890.14271460.12551608516231100

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