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- PDB-3s0q: Peptidase module of the peptidoglycan hydrolase RipA (Rv1477) fro... -

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Basic information

Entry
Database: PDB / ID: 3s0q
TitlePeptidase module of the peptidoglycan hydrolase RipA (Rv1477) from Mycobacterium tuberculosis, catalytic site mutant (Cys383Ala) at 1.45 resolution
ComponentsINVASION PROTEIN
KeywordsHYDROLASE / NlpC/p60 module / peptidoglycan hydrolase
Function / homology
Function and homology information


cell wall organization or biogenesis / N-acetylmuramoyl-L-alanine amidase activity / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / peptidoglycan-based cell wall / cell wall organization / proteolysis / extracellular region
Similarity search - Function
: / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan endopeptidase RipA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBoth, D. / Schnell, R. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Peptidoglycan Remodeling in Mycobacterium tuberculosis: Comparison of Structures and Catalytic Activities of RipA and RipB.
Authors: Both, D. / Schneider, G. / Schnell, R.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: INVASION PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,7071
Polymers22,7071
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.830, 65.850, 68.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INVASION PROTEIN


Mass: 22706.783 Da / Num. of mol.: 1 / Fragment: RipA peptidase module / Mutation: C383A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1477 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53168
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.82 Å3/Da / Density % sol: 32.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% PEG400, 0.2M LiSO4, Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03873 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2011
Details: Multilayer mirror, curved to focus in the vertical (R = 400 m).
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03873 Å / Relative weight: 1
ReflectionResolution: 1.45→18.67 Å / Num. all: 30245 / Num. obs: 29973 / % possible obs: 99.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 4.8 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 15.1
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 4 / Num. unique all: 4098 / Rsym value: 0.375 / % possible all: 94.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→18.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.889 / SU ML: 0.035 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17827 1537 5.1 %RANDOM
Rwork0.15159 ---
obs0.15296 28377 99.4 %-
all-29973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.26 Å2
Refine analyzeLuzzati coordinate error free: 0.067 Å
Refinement stepCycle: LAST / Resolution: 1.45→18.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 0 244 1786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221603
X-RAY DIFFRACTIONr_bond_other_d0.0010.021097
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9712187
X-RAY DIFFRACTIONr_angle_other_deg0.91132672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64422.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.93515246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.271513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_mcbond_it0.861.51037
X-RAY DIFFRACTIONr_mcbond_other0.2411.5434
X-RAY DIFFRACTIONr_mcangle_it1.45521670
X-RAY DIFFRACTIONr_scbond_it2.13566
X-RAY DIFFRACTIONr_scangle_it3.3774.5513
LS refinement shellResolution: 1.449→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 116 -
Rwork0.238 1905 -
obs--92.11 %

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