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

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Basic information

Entry
Database: PDB / ID: 4idy
TitleMycobacterium Tuberculosis Methionine aminopeptidase Type 1c in complex with 2-hydroxyethyl disulfide
ComponentsMethionine aminopeptidase 2Methionyl aminopeptidase
KeywordsHYDROLASE / pita-bread fold / aminopeptidase / 2-hydroxyethylcysteine disulfide
Function / homology
Function and homology information


: / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / 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
2-HYDROXYETHYL DISULFIDE / : / 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 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references

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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)32,0203
Polymers31,8271
Non-polymers1932
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.359, 48.174, 56.662
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31826.904 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-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000 monomethyl ether, BisTris, Oxidized beta-mercaptoethanol, 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→22.16 Å / Num. obs: 17121 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.895 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.192 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20927 872 5.1 %RANDOM
Rwork0.14957 ---
all0.15258 17121 --
obs0.15258 16247 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.163 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→22.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 9 264 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192252
X-RAY DIFFRACTIONr_bond_other_d0.0010.022120
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9523082
X-RAY DIFFRACTIONr_angle_other_deg0.9134876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1223.7596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43815340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3011515
X-RAY DIFFRACTIONr_chiral_restr0.1120.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
LS refinement shellResolution: 1.997→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 56 -
Rwork0.215 1040 -
obs--83.54 %

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