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- PDB-4z7m: Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broa... -

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Basic information

Entry
Database: PDB / ID: 4z7m
TitleNovel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical Activity
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / antibacterial / methionine aminopeptidase / azepinone / structure-based design / drug discovery / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / proteolysis / metal ion binding / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-4L9 / : / Methionine aminopeptidase / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
Model detailsRNA binding protein
AuthorsRose, J.A. / Lahiri, S.D. / McKinney, D.C. / Albert, R. / Morningstar, M. / Shapiro, A.B. / Fisher, S.F. / Fleming, P.R.
CitationJournal: To be Published
Title: Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical Activity
Authors: Rose, J.A. / Lahiri, S.D. / McKinney, D.C. / Albert, R. / Morningstar, M. / Shapiro, A.B. / Fisher, S.F. / Fleming, P.R.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Assembly

Deposited unit
A: Methionine aminopeptidase
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9846
Polymers57,9912
Non-polymers9934
Water6,972387
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4923
Polymers28,9951
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4923
Polymers28,9951
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.985, 62.712, 72.978
Angle α, β, γ (deg.)90.000, 89.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / Methionyl aminopeptidase / MetAP / Peptidase M / MAP


Mass: 28995.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: map, Z0178, ECs0170 / Plasmid: pET50b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3) pLysS
References: UniProt: P0AE20, UniProt: P0AE18*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-4L9 / N~2~-[(3,5-difluorophenyl)acetyl]-N-[(3S,7R)-1-methyl-2-oxo-7-phenyl-2,3,4,7-tetrahydro-1H-azepin-3-yl]-L-alaninamide


Mass: 441.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25F2N3O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM MES, 1.1 M ammonium sulfate, 0.1 M potassium chloride, 9% trehalose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→47.57 Å / Num. obs: 71302 / % possible obs: 92.1 % / Redundancy: 6 % / Net I/σ(I): 4.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
d*TREKdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→47.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.493 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3055 3601 5.1 %RANDOM
Rwork0.2511 ---
obs0.2539 67700 69.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.83 Å2 / Biso mean: 32.034 Å2 / Biso min: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å21.14 Å2
2---3.26 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: final / Resolution: 1.43→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 66 387 4505
Biso mean--28.61 38.22 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194190
X-RAY DIFFRACTIONr_bond_other_d0.0020.024042
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9845662
X-RAY DIFFRACTIONr_angle_other_deg1.04639340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7735520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88324.253174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59215756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9921526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214648
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02862
X-RAY DIFFRACTIONr_mcbond_it2.2792.9752086
X-RAY DIFFRACTIONr_mcbond_other2.2792.9742085
X-RAY DIFFRACTIONr_mcangle_it3.0114.4512604
LS refinement shellResolution: 1.434→1.471 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.609 15 -
Rwork0.749 347 -
all-362 -
obs--4.82 %

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