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- PDB-1y1n: Identification of SH3 motif in M. Tuberculosis methionine aminope... -

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Basic information

Entry
Database: PDB / ID: 1y1n
TitleIdentification of SH3 motif in M. Tuberculosis methionine aminopeptidase suggests a mode of interaction with the ribosome
ComponentsMethionine aminopeptidase 1B
KeywordsHYDROLASE / Methionine aminopeptidase / MtMetAP1B / PxxP / SH3 / ribosome / L24
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
: / Methionine aminopeptidase 2 / Methionine aminopeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsAddlagatta, A. / Quillin, M.L. / Omotoso, O. / Liu, J.O. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 2005
Title: Identification of an SH3-Binding Motif in a New Class of Methionine Aminopeptidases from Mycobacterium tuberculosis Suggests a Mode of Interaction with the Ribosome
Authors: Addlagatta, A. / Quillin, M.L. / Omotoso, O. / Liu, J.O. / Matthews, B.W.
#1: Journal: Chem.Rev. / Year: 2002
Title: Metalloaminopeptidases: Common functional themes in disparate structural surroundings
Authors: Lowther, W.T. / Matthews, B.W.
History
DepositionNov 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: Methionine aminopeptidase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7902
Polymers31,7511
Non-polymers391
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.335, 47.908, 56.819
Angle α, β, γ (deg.)90.00, 95.11, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsBiological unit is a monomer as seen in the assyemetric unit

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Components

#1: Protein Methionine aminopeptidase 1B / E.C.3.4.11.18 / MAP / Peptidase M


Mass: 31750.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Description: N-terminal His-tag was kept during crystallization but is not visible in the elecron density maps
Gene: map, mapB / Plasmid: pET28a MtMetAP1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A5J2, UniProt: P9WK19*PLUS, methionyl aminopeptidase
#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 6.5
Details: Bistris, PEG monomethyl ether 2000, KCl, HEPES, NaCl, pH 6.5, VAPOR DIFFUSION, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.51→20 Å / Num. all: 41440 / Num. obs: 41440 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 30.6
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 7.67 / Num. unique all: 4038 / Rsym value: 0.154 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C21

1c21


Resolution: 1.51→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2032 -random
Rwork0.2019 ---
all0.213 41425 --
obs0.213 40517 97.3 %-
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.012 Å20 Å2-0.527 Å2
2---8.2 Å20 Å2
3---2.188 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 1 329 2483
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006868
X-RAY DIFFRACTIONc_angle_deg1.40134
X-RAY DIFFRACTIONc_mcbond_it3.1441.5
X-RAY DIFFRACTIONc_scbond_it4.5212
X-RAY DIFFRACTIONc_mcangle_it3.7722
X-RAY DIFFRACTIONc_scangle_it5.5062.5
LS refinement shellResolution: 1.51→1.56 Å
RfactorNum. reflection% reflection
Rfree0.3166 207 -
Rwork0.2764 --
obs-3556 0.8579 %

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