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- PDB-4m6g: Structure of the Mycobacterium tuberculosis peptidoglycan amidase... -

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Basic information

Entry
Database: PDB / ID: 4m6g
TitleStructure of the Mycobacterium tuberculosis peptidoglycan amidase Rv3717 in complex with L-Alanine-iso-D-Glutamine reaction product
ComponentsPeptidoglycan Amidase Rv3717
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / TB Structural Genomics Consortium / TBSGC / Zn Binding
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / cell wall macromolecule catabolic process / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE / D-alpha-glutamine / N-acetylmuramoyl-L-alanine amidase Rv3717 / N-acetymuramyl-L-alanine amidase-related protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 Å
AuthorsPrigozhin, D.M. / Mavrici, D. / Huizar, J.P. / Vansell, H.J. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Biochemical Analyses of Mycobacterium tuberculosis N-Acetylmuramyl-L-alanine Amidase Rv3717 Point to a Role in Peptidoglycan Fragment Recycling.
Authors: Prigozhin, D.M. / Mavrici, D. / Huizar, J.P. / Vansell, H.J. / Alber, T.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 2.0May 16, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_asym.entity_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_site.details / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Sep 20, 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_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_atom_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_atom_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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan Amidase Rv3717
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7985
Polymers23,4321
Non-polymers3664
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-21 kcal/mol
Surface area8580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.982, 75.958, 49.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peptidoglycan Amidase Rv3717 / N-acetylmuramoyl-L-alanine amidase Rv3717


Mass: 23432.195 Da / Num. of mol.: 1 / Fragment: UNP residues 20-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3717 / Production host: Escherichia coli (E. coli)
References: UniProt: I6Y4D2, UniProt: O69684*PLUS, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical ChemComp-ZGL / D-alpha-glutamine / Iso-D-glutamine / Isoglutamine


Type: D-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM sodium chloride, 100 mM TRIS, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12482 / % possible obs: 97.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.44 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.27 / Rsym value: 0.527 / % possible all: 87.31

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Processing

Software
NameClassification
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NE8

3ne8


Resolution: 2.104→45.065 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 628 5.05 %
Rwork0.2063 --
obs0.2082 12431 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.104→45.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 2 66 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081614
X-RAY DIFFRACTIONf_angle_d0.852189
X-RAY DIFFRACTIONf_dihedral_angle_d11.804583
X-RAY DIFFRACTIONf_chiral_restr0.046237
X-RAY DIFFRACTIONf_plane_restr0.002300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.104-2.31610.34271480.262682X-RAY DIFFRACTION90
2.3161-2.65120.28571560.22222953X-RAY DIFFRACTION99
2.6512-3.34010.23351580.20583010X-RAY DIFFRACTION100
3.3401-45.07530.21151660.18673158X-RAY DIFFRACTION100

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