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- PDB-3pkb: M. tuberculosis MetAP with bengamide analog Y16, in Mn form -

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Basic information

Entry
Database: PDB / ID: 3pkb
TitleM. tuberculosis MetAP with bengamide analog Y16, in Mn form
ComponentsMethionine aminopeptidase
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


: / methionyl aminopeptidase / initiator methionyl aminopeptidase activity / 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-Y16 / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 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 1.2Feb 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_seq_id / _struct_conn.ptnr2_label_asym_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)31,4826
Polymers30,9221
Non-polymers5605
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Methionine aminopeptidase
hetero molecules

A: Methionine aminopeptidase
hetero molecules

A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,44518
Polymers92,7663
Non-polymers1,67915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area4800 Å2
ΔGint-68 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.952, 105.952, 50.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-473-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methionine 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

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Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-Y16 / (E,2R,3R,4S,5R)-N-(2-azanyl-2-oxidanylidene-ethyl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide


Mass: 318.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H26N2O6
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, pH 5.5, 1.3M AMS, 10% glycerol, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorDate: Mar 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 85942

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.54 Å33.85 Å
Translation1.54 Å33.85 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→33.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1795 / WRfactor Rwork: 0.1658 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8952 / SU B: 0.547 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0395 / SU Rfree: 0.0401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 4291 5 %RANDOM
Rwork0.168 ---
obs0.1687 85822 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.31 Å2 / Biso mean: 13.6797 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 30 211 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222242
X-RAY DIFFRACTIONr_angle_refined_deg2.4891.9623067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29323.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5341515
X-RAY DIFFRACTIONr_chiral_restr0.3030.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211710
X-RAY DIFFRACTIONr_mcbond_it1.2131.51411
X-RAY DIFFRACTIONr_mcangle_it2.06522293
X-RAY DIFFRACTIONr_scbond_it3.0983831
X-RAY DIFFRACTIONr_scangle_it4.5644.5774
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 234 -
Rwork0.278 4749 -
all-4983 -
obs--76.63 %

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