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- PDB-5yoh: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C10... -

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Basic information

Entry
Database: PDB / ID: 5yoh
TitleMycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105M mutant) in complex with Methionine
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / Methionine aminopeptidase
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / proteolysis / 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
: / METHIONINE / Methionine aminopeptidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsSandeep, C.B. / Addlagatta, A.
Funding support India, 1items
OrganizationGrant numberCountry
Deparment of science and TechnologyEMR/2015/000461 India
CitationJournal: To Be Published
Title: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105M mutant) in complex with Methionine
Authors: Sandeep, C.B. / Addlagatta, A.
History
DepositionOct 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Nov 22, 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
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

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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)34,8536
Polymers34,4711
Non-polymers3825
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.332, 48.690, 56.151
Angle α, β, γ (deg.)90.000, 95.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methionine aminopeptidase / MetAP / Peptidase M


Mass: 34470.824 Da / Num. of mol.: 1 / Mutation: C105M, C284A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Strain: H37Ra / Gene: mapB, map, MRA_2886 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U6L5, methionyl aminopeptidase

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Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 27% Peg3350, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.62→28.59 Å / Num. obs: 32311 / % possible obs: 92.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.026 / Rrim(I) all: 0.038 / Χ2: 1.028 / Net I/av σ(I): 18.94 / Net I/σ(I): 59.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.680.11831140.9610.1170.1661.07178.1
1.68-1.750.0940.970.0920.1321.00590.6
1.75-1.820.0760.9790.0750.1071.00191.2
1.82-1.920.060.9870.0590.0841.01891.9
1.92-2.040.0460.9920.0450.0651.08892.2
2.04-2.20.0360.9940.0350.051.02893.5
2.2-2.420.0280.9960.0280.041.02794.5
2.42-2.770.0260.9970.0250.0361.03396
2.77-3.490.0260.9970.0250.0361.01296.3
3.49-3.70.0220.9970.0220.0311.00697.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.38
Highest resolutionLowest resolution
Rotation28.59 Å1.89 Å

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Processing

Software
NameVersionClassification
SCALEPACK2.2.0data scaling
MOLREP11.4.03model building
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
DENZO2.3.1data reduction
HKL-20002.3.1data collection
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YJ3

1yj3


Resolution: 1.63→28.59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.552 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1526 4.7 %RANDOM
Rwork0.166 ---
obs0.1683 32306 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.9 Å2 / Biso mean: 23.683 Å2 / Biso min: 11.41 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.63→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 18 208 2380
Biso mean--25.47 29.52 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192272
X-RAY DIFFRACTIONr_bond_other_d0.0020.022157
X-RAY DIFFRACTIONr_angle_refined_deg2.1591.9563117
X-RAY DIFFRACTIONr_angle_other_deg1.09434964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80423.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75615351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0461515
X-RAY DIFFRACTIONr_chiral_restr0.1320.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212607
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02500
LS refinement shellResolution: 1.625→1.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 91 -
Rwork0.262 2175 -
all-2266 -
obs-3114 92.53 %

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