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- PDB-4m6h: Structure of the reduced, metal-free form of Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 4m6h
TitleStructure of the reduced, metal-free 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 / molecular replacement / Resolution: 2.194 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 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)46,8642
Polymers46,8642
Non-polymers00
Water1,42379
1
A: Peptidoglycan Amidase Rv3717


Theoretical massNumber of molelcules
Total (without water)23,4321
Polymers23,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan Amidase Rv3717


Theoretical massNumber of molelcules
Total (without water)23,4321
Polymers23,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.358, 45.677, 67.789
Angle α, β, γ (deg.)90.000, 116.020, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.86 Å3/Da / Density % sol: 33.9 %
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: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.194→42.33 Å / Num. obs: 17421 / % possible obs: 97.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 29.27 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.048 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.194-2.242.30.5198560.789196.2
2.24-2.282.30.5358790.83196.3
2.28-2.322.30.4698460.841196.4
2.32-2.372.30.428360.88196.6
2.37-2.422.30.3458810.921196.7
2.42-2.482.30.3298530.879196.9
2.48-2.542.30.3248491196.7
2.54-2.612.30.2848640.964197
2.61-2.692.30.2638551.047197.2
2.69-2.772.30.2078580.971196.9
2.77-2.872.30.1818730.996197.7
2.87-2.992.30.1648751.101197.7
2.99-3.122.30.1368661.109197.4
3.12-3.292.30.118731.248197.8
3.29-3.492.30.0898881.317197.8
3.49-3.762.30.0678671.386198.1
3.76-4.142.20.0568831.354197.9
4.14-4.742.20.0478831.29197.9
4.74-5.972.20.0388971.018197.4
5.97-42.332.20.0269391.023199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3ne8


Resolution: 2.194→42.33 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8227 / SU ML: 0.27 / σ(F): 0 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1629 9.99 %
Rwork0.2046 --
obs0.2075 16314 90.96 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.76 Å2 / Biso mean: 37.4756 Å2 / Biso min: 18.97 Å2
Refinement stepCycle: LAST / Resolution: 2.194→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 0 79 2678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052645
X-RAY DIFFRACTIONf_angle_d1.1863586
X-RAY DIFFRACTIONf_chiral_restr0.061396
X-RAY DIFFRACTIONf_plane_restr0.005484
X-RAY DIFFRACTIONf_dihedral_angle_d12.299958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.194-2.27240.34841500.28341305145581
2.2724-2.36340.30171480.25781347149585
2.3634-2.47090.2951590.24051393155287
2.4709-2.60120.28791480.24011407155588
2.6012-2.76410.27911540.22831428158290
2.7641-2.97750.25591660.2181485165192
2.9775-3.2770.23941740.22131526170095
3.277-3.75090.21221720.18951560173297
3.7509-4.72480.18591770.1651589176698
4.7248-42.33770.20111810.18761645182698

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