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- PDB-2ggc: Novel bacterial methionine aminopeptidase inhibitors -

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Basic information

Entry
Database: PDB / ID: 2ggc
TitleNovel bacterial methionine aminopeptidase inhibitors
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / methionine amino peptidase / pita-bread fold / MAP inhibitor / antibacterial
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / ferrous iron binding / proteolysis / 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
: / METHIONINE / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsEvdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M.
CitationJournal: Proteins / Year: 2007
Title: Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors.
Authors: Evdokimov, A.G. / Pokross, M. / Walter, R.L. / Mekel, M. / Barnett, B.L. / Amburgey, J. / Seibel, W.L. / Soper, S.J. / Djung, J.F. / Fairweather, N. / Diven, C. / Rastogi, V. / Grinius, L. / ...Authors: Evdokimov, A.G. / Pokross, M. / Walter, R.L. / Mekel, M. / Barnett, B.L. / Amburgey, J. / Seibel, W.L. / Soper, S.J. / Djung, J.F. / Fairweather, N. / Diven, C. / Rastogi, V. / Grinius, L. / Klanke, C. / Siehnel, R. / Twinem, T. / Andrews, R. / Curnow, A.
History
DepositionMar 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_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_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_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_conn.ptnr2_label_seq_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: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5305
Polymers29,2401
Non-polymers2904
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.754, 59.468, 51.197
Angle α, β, γ (deg.)90.00, 111.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / MAP / Peptidase M


Mass: 29239.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: map / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AE18, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 1.87 Å3/Da / Density % sol: 34.39 %
Crystal growTemperature: 298 K / Method: batch / pH: 7
Details: 10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→23.8 Å / Num. all: 98330 / Num. obs: 98330 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 28.1
Reflection shellResolution: 1→1.15 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 11.2 / Num. unique all: 17489 / % possible all: 73.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GG0

2gg0


Resolution: 1→23.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.498 / SU ML: 0.012 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.025 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.133 4955 5 %RANDOM
Rwork0.12 ---
all0.12 98330 --
obs0.12 98330 84.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.287 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.02 Å2
2--0.11 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 12 345 2668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222400
X-RAY DIFFRACTIONr_bond_other_d0.0010.022240
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9713305
X-RAY DIFFRACTIONr_angle_other_deg0.71835277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4675339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74224.159113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71315465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3691519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022746
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02475
X-RAY DIFFRACTIONr_nbd_refined0.3430.2563
X-RAY DIFFRACTIONr_nbd_other0.2250.22448
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21194
X-RAY DIFFRACTIONr_nbtor_other0.0880.21300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1050.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1870.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3670.248
X-RAY DIFFRACTIONr_mcbond_it1.2381.51457
X-RAY DIFFRACTIONr_mcbond_other0.5631.5593
X-RAY DIFFRACTIONr_mcangle_it1.92822423
X-RAY DIFFRACTIONr_scbond_it2.4113962
X-RAY DIFFRACTIONr_scangle_it3.5674.5846
X-RAY DIFFRACTIONr_rigid_bond_restr1.02634740
X-RAY DIFFRACTIONr_sphericity_free6.2053348
X-RAY DIFFRACTIONr_sphericity_bonded2.65534560
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 103 -
Rwork0.373 1755 -
obs-1858 21.8 %

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