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- PDB-4m6i: Structure of the reduced, Zn-bound form of Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 4m6i
TitleStructure of the reduced, Zn-bound form of Mycobacterium tuberculosis peptidoglycan amidase Rv3717
ComponentsPeptidoglycan Amidase Rv3717
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan 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
N-acetymuramyl-L-alanine amidase-related protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.666 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 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan Amidase Rv3717
B: Peptidoglycan Amidase Rv3717
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9954
Polymers46,8642
Non-polymers1312
Water32418
1
A: Peptidoglycan Amidase Rv3717
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4982
Polymers23,4321
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan Amidase Rv3717
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4982
Polymers23,4321
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.427, 45.935, 68.050
Angle α, β, γ (deg.)90.000, 116.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidoglycan Amidase Rv3717 / N-acetymuramyl-L-alanine amidase-related protein


Mass: 23432.195 Da / Num. of mol.: 2 / Fragment: UNP residues 20-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3820, Rv3717 / Production host: Escherichia coli (E. coli)
References: UniProt: O69684, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.87 Å3/Da / Density % sol: 34.4 %
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: 1.283055 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283055 Å / Relative weight: 1
ReflectionResolution: 2.666→50 Å / Num. obs: 10030 / % possible obs: 98.2 % / Redundancy: 7.5 % / Biso Wilson estimate: 43.44 Å2 / Rmerge(I) obs: 0.144 / Χ2: 0.977 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.666-2.725.10.7773710.754171.5
2.72-2.7760.734590.759195.4
2.77-2.826.40.6635040.811198.8
2.82-2.8870.615080.901199.8
2.88-2.947.40.5335140.841100
2.94-3.017.70.4734910.9391100
3.01-3.087.90.4315140.9421100
3.08-3.177.80.3785050.9791100
3.17-3.2680.2985081.0251100
3.26-3.367.90.2575121.031100
3.36-3.487.90.2084950.991100
3.48-3.627.90.1644991.0151100
3.62-3.7980.1415201.0911100
3.79-3.997.90.1234991.1081100
3.99-4.247.90.0995280.9721100
4.24-4.567.90.0885191.0531100
4.56-5.027.80.0894951.0731100
5.02-5.757.80.0965261.061199.8
5.75-7.247.60.0865161.035199.6
7.24-507.50.0655470.9051100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NE8

3ne8


Resolution: 2.666→42.524 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8285 / SU ML: 0.33 / σ(F): 0.35 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2232 980 10.08 %
Rwork0.197 --
obs0.1997 9721 95.98 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.93 Å2 / Biso mean: 35.5794 Å2 / Biso min: 2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.666→42.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 2 18 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052715
X-RAY DIFFRACTIONf_angle_d1.1023679
X-RAY DIFFRACTIONf_chiral_restr0.064404
X-RAY DIFFRACTIONf_plane_restr0.005495
X-RAY DIFFRACTIONf_dihedral_angle_d12.003979
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.666-2.80650.29391220.28061079120185
2.8065-2.98230.27981400.25291220136095
2.9823-3.21250.26781420.23951244138697
3.2125-3.53560.26181420.20871276141898
3.5356-4.04690.1871420.17141282142499
4.0469-5.09730.17081450.16031298144399
5.0973-42.5290.22681470.18991342148999

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