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- PDB-3iu9: M. tuberculosis methionine aminopeptidase with Ni inhibitor T07 -

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Basic information

Entry
Database: PDB / ID: 3iu9
TitleM. tuberculosis methionine aminopeptidase with Ni inhibitor T07
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / enzyme-inhibitor complex / Aminopeptidase / Cobalt / Metal-binding / Protease
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-T07 / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsYe, Q.Z. / Lu, J.P.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Catalysis and Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidase
Authors: Lu, J.P. / Chai, S.C. / Ye, Q.Z.
History
DepositionAug 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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)31,7356
Polymers31,2111
Non-polymers5245
Water3,477193
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)95,20618
Polymers93,6343
Non-polymers1,57215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3930 Å2
ΔGint-17 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.216, 106.216, 50.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methionine aminopeptidase / MAP / Peptidase M


Mass: 31211.256 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, 198 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-T07 / 5-[(2,4-dichlorobenzyl)sulfanyl]-4H-1,2,4-triazol-3-amine


Mass: 275.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8Cl2N4S
#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.: 193 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 1.3 M AMS, 15% glycerol, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorDate: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 32971 / % possible obs: 99.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.078 / Χ2: 4.045 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.786.90.17514892.44892.2
1.78-1.818.20.1716742.703100
1.81-1.859.10.17616083.056100
1.85-1.899.20.1616623.549100
1.89-1.939.30.14816473.658100
1.93-1.979.30.13816543.93799.9
1.97-2.029.30.12616443.917100
2.02-2.079.40.11716354.119100
2.07-2.149.40.11116634.169100
2.14-2.29.40.10316414.525100
2.2-2.289.40.09916544.519100
2.28-2.389.40.09416514.25100
2.38-2.489.50.0916624.36100
2.48-2.619.40.08616584.347100
2.61-2.789.40.08116654.393100
2.78-2.999.40.07416544.62599.9
2.99-3.299.40.06816614.67100
3.29-3.779.30.06116764.74599.7
3.77-4.759.10.05316794.34299.5
4.75-508.60.0516943.68697.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å34.1 Å
Translation1.95 Å34.1 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YJ3

1yj3


Resolution: 1.75→34.09 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.887 / SU B: 1.692 / SU ML: 0.056 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1666 5.1 %RANDOM
Rwork0.164 ---
obs0.165 32958 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.35 Å2 / Biso mean: 14.566 Å2 / Biso min: 4.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 24 193 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222238
X-RAY DIFFRACTIONr_angle_refined_deg2.3091.963061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96623.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76115337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9471515
X-RAY DIFFRACTIONr_chiral_restr0.190.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211714
X-RAY DIFFRACTIONr_mcbond_it1.3021.51411
X-RAY DIFFRACTIONr_mcangle_it2.09422293
X-RAY DIFFRACTIONr_scbond_it3.3923827
X-RAY DIFFRACTIONr_scangle_it5.2764.5768
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 102 -
Rwork0.176 2187 -
all-2289 -
obs--95.1 %

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