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- PDB-3pkc: M. tuberculosis MetAP with bengamide analog Y08, in Mn form -

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Basic information

Entry
Database: PDB / ID: 3pkc
TitleM. tuberculosis MetAP with bengamide analog Y08, in Mn form
ComponentsMethionine aminopeptidaseMethionyl aminopeptidase
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


: / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / cobalt ion binding / metalloaminopeptidase activity / protein processing / iron ion binding / 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-Y08 / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsYe, Q.Z. / Lu, J.P.
CitationJournal: Chemmedchem / Year: 2011
Title: Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.
Authors: Lu, J.P. / Yuan, X.H. / Yuan, H. / Wang, W.L. / Wan, B. / Franzblau, S.G. / Ye, Q.Z.
History
DepositionNov 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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)31,4584
Polymers30,9221
Non-polymers5363
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.667, 79.945, 65.055
Angle α, β, γ (deg.)90.000, 91.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

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


Mass: 30921.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: map, mapB, MT2929, MTV003.07c, Rv2861c / Plasmid: pGEMEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A5J2, UniProt: P9WK19*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-Y08 / (E,2R,3R,4S,5R)-N-[[(3S)-1-cyclopropylcarbonylpiperidin-3-yl]methyl]-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide


Mass: 426.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N2O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, pH 5.5, 1.3M Ammonium Sulfate, 10% glycerol, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorDate: Oct 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 45772 / % possible obs: 91.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.075 / Χ2: 1.718 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.47-1.540.48124730.86198.4
1.5-1.524.70.38624880.8971100
1.52-1.554.90.33924930.9051100
1.55-1.584.90.29225050.9071100
1.58-1.624.90.25525000.9521100
1.62-1.664.90.22524931.0251100
1.66-1.74.90.18725421.0571100
1.7-1.7450.16224631.1471100
1.74-1.7950.14224951.1561100
1.79-1.8550.12424841.3171100
1.85-1.924.60.11415171.39159.7
1.92-24.70.09317061.712168.7
2-2.0950.08325061.86199.9
2.09-2.250.07525151.9431100
2.2-2.334.50.06711362.068145
2.33-2.5150.06624972.267199.8
2.51-2.774.90.0725042.978199.8
2.77-3.174.80.06624983.628199
3.17-3.994.30.05515033.545159.6
3.99-504.70.05324543.621195.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.67 Å28.82 Å
Translation1.67 Å28.82 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→28.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2155 / WRfactor Rwork: 0.1853 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.881 / SU B: 0.991 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0743 / SU Rfree: 0.0774 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2324 5.1 %RANDOM
Rwork0.1839 ---
obs0.1855 45770 90.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.37 Å2 / Biso mean: 17.0347 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.47→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 32 167 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222225
X-RAY DIFFRACTIONr_angle_refined_deg2.3891.9633044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1523.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89515334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9891515
X-RAY DIFFRACTIONr_chiral_restr0.1970.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211698
X-RAY DIFFRACTIONr_mcbond_it1.4421.51394
X-RAY DIFFRACTIONr_mcangle_it2.21422265
X-RAY DIFFRACTIONr_scbond_it3.5093831
X-RAY DIFFRACTIONr_scangle_it5.1584.5776
LS refinement shellResolution: 1.47→1.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 195 -
Rwork0.241 3305 -
all-3500 -
obs--95.08 %

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