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- PDB-3pke: M. tuberculosis MetAP with bengamide analog Y10, in Ni form -

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Basic information

Entry
Database: PDB / ID: 3pke
TitleM. tuberculosis MetAP with bengamide analog Y10, in Ni 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
NICKEL (II) ION / Chem-Y10 / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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_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)31,5486
Polymers30,9221
Non-polymers6265
Water3,225179
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)94,64518
Polymers92,7663
Non-polymers1,87915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area4860 Å2
ΔGint-68 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.454, 105.454, 50.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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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, 184 molecules

#2: Chemical ChemComp-Y10 / (E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide


Mass: 377.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H31NO5
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
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: Jul 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 41930 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.153 / Χ2: 1.391 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.636.10.81321001.1541100
1.63-1.666.10.74720551.1981100
1.66-1.696.10.6621101.1961100
1.69-1.726.10.5921031.2311100
1.72-1.766.10.53220781.2071100
1.76-1.86.20.47721021.2671100
1.8-1.856.20.41820961.2151100
1.85-1.96.20.36820831.3891100
1.9-1.956.10.35221201.9041100
1.95-2.026.20.24620921.2951100
2.02-2.096.20.25821001.8181100
2.09-2.176.20.18521121.3261100
2.17-2.276.20.19620871.7441100
2.27-2.396.30.14921131.3131100
2.39-2.546.30.13721051.3111100
2.54-2.746.30.12521031.3711100
2.74-3.016.30.0921341.2921100
3.01-3.456.30.06920991.385199.1
3.45-4.346.40.05520841.449198
4.34-506.40.05720541.74193.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.77 Å25.06 Å
Translation1.77 Å25.06 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: 1.6→25.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.1843 / WRfactor Rwork: 0.1547 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8901 / SU B: 1.373 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0789 / SU Rfree: 0.0829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 2120 5.1 %RANDOM
Rwork0.1725 ---
obs0.1743 41911 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.06 Å2 / Biso mean: 11.027 Å2 / Biso min: 2.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 35 179 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222249
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.9663078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20823.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4981515
X-RAY DIFFRACTIONr_chiral_restr0.1770.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211715
X-RAY DIFFRACTIONr_mcbond_it1.2841.51413
X-RAY DIFFRACTIONr_mcangle_it2.05622297
X-RAY DIFFRACTIONr_scbond_it3.4243836
X-RAY DIFFRACTIONr_scangle_it4.8834.5781
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 156 -
Rwork0.241 2920 -
all-3076 -
obs--100 %

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