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

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Basic information

Entry
Database: PDB / ID: 2ggb
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
: / Chem-U17 / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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

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Assembly

Deposited unit
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7565
Polymers29,2401
Non-polymers5164
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.722, 61.454, 53.308
Angle α, β, γ (deg.)90.00, 107.08, 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-U17 / METHYL N-[(2S,3R)-3-AMINO-2-HYDROXYHEPTANOYL]-L-SERYL-L-LEUCINATE / 2-[2-(3-AMINO-2-HYDROXY-HEPTANOYLAMINO)-3-HYDROXY-PROPIONYLAMINO]-4-METHYL-PENTANOIC ACID METHYL ESTER


Mass: 375.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H33N3O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 298 K / pH: 7
Details: 10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, batch, pH 7.0, 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: 2.13→30.73 Å / Num. all: 13433 / Num. obs: 13433 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 25.4
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 10.9 / Num. unique all: 2012 / % possible all: 99.3

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Processing

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

2gg0


Resolution: 2.13→30.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.179 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 663 4.9 %RANDOM
Rwork0.185 ---
all0.189 13433 --
obs0.185 13433 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.039 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å2-0.76 Å2
2--1.43 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.13→30.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 29 107 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222152
X-RAY DIFFRACTIONr_angle_refined_deg2.361.9812916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8875276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28524.31695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.11715395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.371515
X-RAY DIFFRACTIONr_chiral_restr0.1720.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021601
X-RAY DIFFRACTIONr_nbd_refined0.2430.21096
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2127
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.25
X-RAY DIFFRACTIONr_mcbond_it1.7591.51324
X-RAY DIFFRACTIONr_mcangle_it2.64922162
X-RAY DIFFRACTIONr_scbond_it4.7243841
X-RAY DIFFRACTIONr_scangle_it6.6274.5747
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 43 -
Rwork0.229 913 -
obs-956 98.56 %

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