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- PDB-4km3: Discovery of a novel structural motif in methionine aminopeptidas... -

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Basic information

Entry
Database: PDB / ID: 4km3
TitleDiscovery of a novel structural motif in methionine aminopeptidase from Streptococci with possible post-translational modification
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / Classification
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M24A, methionine aminopeptidase, subfamily 1 / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Methionine aminopeptidase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsArya, T. / Addlagatta, A.
CitationJournal: Plos One / Year: 2013
Title: Discovery of a new genetic variant of methionine aminopeptidase from streptococci with possible post-translational modifications: biochemical and structural characterization.
Authors: Arya, T. / Kishor, C. / Saddanapu, V. / Reddi, R. / Addlagatta, A.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine aminopeptidase
B: Methionine aminopeptidase


Theoretical massNumber of molelcules
Total (without water)63,3982
Polymers63,3982
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-11 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.687, 109.687, 164.424
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Methionine aminopeptidase


Mass: 31699.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: CGSP14 / Gene: map, SPCG_1194 / Production host: Escherichia coli (E. coli) / References: UniProt: B2IQ22
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 4.5 Å3/Da / Density % sol: 72.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic , pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 3, 2013
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.7326
11K,H,-L20.2674
ReflectionResolution: 3.2→23.75 Å / Num. obs: 18507 / % possible obs: 91.64 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.493 / Rsym value: 0.7 / % possible all: 91.64

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TB5

3tb5


Resolution: 3.2→23.75 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.815 / SU B: 22.316 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.498 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28493 875 5.2 %RANDOM
Rwork0.20997 ---
obs0.2138 16111 91.64 %-
all-16111 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.278 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.2→23.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 0 20 4378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194440
X-RAY DIFFRACTIONr_bond_other_d0.0010.024203
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9665998
X-RAY DIFFRACTIONr_angle_other_deg0.83239703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3555560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52424.9200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36715782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.351523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02953
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 26 -
Rwork0.247 534 -
obs--41.45 %

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