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- PDB-3iu7: M. tuberculosis methionine aminopeptidase with Mn inhibitor A02 -

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Basic information

Entry
Database: PDB / ID: 3iu7
TitleM. tuberculosis methionine aminopeptidase with Mn inhibitor A02
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
5-(2-CHLOROPHENYL)FURAN-2-CARBOXYLIC ACID / : / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 / pdbx_struct_conn_angle / 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 / _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_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)31,8987
Polymers31,2111
Non-polymers6876
Water4,486249
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)95,69421
Polymers93,6343
Non-polymers2,06018
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 area3930 Å2
ΔGint-20 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.412, 106.412, 50.422
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-472-

HOH

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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, 255 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FCD / 5-(2-CHLOROPHENYL)FURAN-2-CARBOXYLIC ACID


Mass: 222.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H7ClO3
#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.: 249 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 1.1 M AMS, 50 mM NaCl, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorDate: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 10 % / Av σ(I) over netI: 43.78 / Number: 642578 / Rmerge(I) obs: 0.045 / Χ2: 0.66 / D res high: 1.4 Å / D res low: 50 Å / Num. obs: 64180 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.85098.810.0240.47610.6
3.023.899.710.030.7327.6
2.633.0210010.0360.7359.6
2.392.6310010.0370.67510.2
2.222.3910010.061.20310
2.092.2210010.0410.57810.3
1.992.0910010.0450.53110.4
1.91.9910010.070.98310.3
1.831.910010.0670.73210.3
1.761.8310010.0690.63910.3
1.711.7610010.0750.55310.3
1.661.7110010.0810.52910.3
1.621.6610010.0920.54710.3
1.581.6210010.1030.55510.3
1.541.5810010.1140.55310.3
1.511.5410010.1260.58510.3
1.481.5110010.1490.62710.3
1.451.4810010.160.57310.2
1.421.4510010.1840.6589.8
1.41.4210010.2150.7458.3
ReflectionResolution: 1.4→50 Å / Num. obs: 64180 / % possible obs: 99.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.045 / Χ2: 0.657 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.428.30.21531710.745100
1.42-1.459.80.18431910.658100
1.45-1.4810.20.1632010.573100
1.48-1.5110.30.14931920.627100
1.51-1.5410.30.12631930.585100
1.54-1.5810.30.11431900.553100
1.58-1.6210.30.10332070.555100
1.62-1.6610.30.09231930.547100
1.66-1.7110.30.08132080.529100
1.71-1.7610.30.07531850.553100
1.76-1.8310.30.06931970.639100
1.83-1.910.30.06732240.732100
1.9-1.9910.30.0731920.983100
1.99-2.0910.40.04532150.531100
2.09-2.2210.30.04132160.578100
2.22-2.39100.0632091.203100
2.39-2.6310.20.03732110.675100
2.63-3.029.60.03632500.735100
3.02-3.87.60.0332500.73299.7
3.8-5010.60.02432850.47698.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.54 Å21.14 Å
Translation1.54 Å21.14 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: 1.4→21.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.898 / SU B: 0.664 / SU ML: 0.028 / SU R Cruickshank DPI: 0.054 / SU Rfree: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3237 5.1 %RANDOM
Rwork0.171 ---
obs0.172 63914 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.12 Å2 / Biso mean: 11.941 Å2 / Biso min: 4.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 38 249 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222253
X-RAY DIFFRACTIONr_angle_refined_deg2.5161.9673082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35123.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5561515
X-RAY DIFFRACTIONr_chiral_restr0.160.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211736
X-RAY DIFFRACTIONr_mcbond_it1.2681.51411
X-RAY DIFFRACTIONr_mcangle_it2.08322293
X-RAY DIFFRACTIONr_scbond_it3.1533842
X-RAY DIFFRACTIONr_scangle_it4.6554.5789
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 264 -
Rwork0.24 4424 -
all-4688 -
obs--99.53 %

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