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- PDB-4if7: Mycobacterium Tuberculosis Methionine aminopeptidase Type 1c in c... -

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Basic information

Entry
Database: PDB / ID: 4if7
TitleMycobacterium Tuberculosis Methionine aminopeptidase Type 1c in complex with homocysteine-methyl disulfide
ComponentsMethionine aminopeptidase 2
KeywordsHYDROLASE / pita-bread fold / aminopeptidase / cobalt
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
: / (2S)-2-amino-4-(methyldisulfanyl)butanoic acid / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReddi, R. / Gumpena, R. / Kishor, C. / Addlagatta, A.
CitationJournal: Febs J. / Year: 2014
Title: Selective targeting of the conserved active site cysteine of Mycobacterium tuberculosis methionine aminopeptidase with electrophilic reagents
Authors: Reddi, R. / Arya, T. / Kishor, C. / Gumpena, R. / Ganji, R.J. / Bhukya, S. / Addlagatta, A.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn ...pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _struct_conn_type.id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0964
Polymers31,7971
Non-polymers2993
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.380, 48.216, 56.400
Angle α, β, γ (deg.)90.00, 95.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase 2 / MAP / Peptidase M


Mass: 31796.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: map / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5J2, UniProt: P9WK19*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-HCM / (2S)-2-amino-4-(methyldisulfanyl)butanoic acid / S-methylsulfanyl-homocystein


Type: L-peptide linking / Mass: 181.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Bistris, PEG monomethyl ether 2000, KCl, HEPES, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25.41 Å / Num. all: 17008 / Num. obs: 16149 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.92 Å / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.111 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.241 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26644 855 5 %RANDOM
Rwork0.20122 ---
all0.20462 17008 --
obs0.20462 16149 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.07 Å2
2--0.17 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→25.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 12 118 2285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192242
X-RAY DIFFRACTIONr_bond_other_d0.0010.022110
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9543068
X-RAY DIFFRACTIONr_angle_other_deg0.8833.0014841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34323.85496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39315340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0161515
X-RAY DIFFRACTIONr_chiral_restr0.10.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 64 -
Rwork0.324 1144 -
obs--91.38 %

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