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- PDB-4q4n: Structure of the Resuscitation Promoting Factor Interacting prote... -

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Basic information

Entry
Database: PDB / ID: 4q4n
TitleStructure of the Resuscitation Promoting Factor Interacting protein RipA mutated at H432
ComponentsPeptidoglycan endopeptidase RipA
KeywordsHYDROLASE / alpha-beta
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 / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsSqueglia, F. / Ruggiero, A. / Romano, M. / Vitagliano, L. / Berisio, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Mutational and structural study of RipA, a key enzyme in Mycobacterium tuberculosis cell division: evidence for the L-to-D inversion of configuration of the catalytic cysteine.
Authors: Squeglia, F. / Ruggiero, A. / Romano, M. / Vitagliano, L. / Berisio, R.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
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: Peptidoglycan endopeptidase RipA


Theoretical massNumber of molelcules
Total (without water)49,7941
Polymers49,7941
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.702, 65.492, 68.330
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 Peptidoglycan endopeptidase RipA / Macrophage invasion and intracellular persistence protein A / Resuscitation-promoting factor ...Macrophage invasion and intracellular persistence protein A / Resuscitation-promoting factor interaction partner A / Rpf-interacting protein A


Mass: 49793.797 Da / Num. of mol.: 1 / Fragment: RipA / Mutation: H432A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ripA, Rv1477 / Production host: Escherichia coli (E. coli)
References: UniProt: O53168, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 8 mg mL-1 protein concentration, 8% (v/v) 2-Propanol, 16% (w/v) PEG4000 in 60 mM Sodium citrate trihydrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 4, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.38→30 Å / Num. all: 33325 / Num. obs: 32925 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.38→1.43 Å / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.803 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18555 1643 5 %RANDOM
Rwork0.16936 ---
obs0.17019 31001 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.38→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 0 284 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221581
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9742150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5942360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.8511512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221218
X-RAY DIFFRACTIONr_mcbond_it0.4951.51027
X-RAY DIFFRACTIONr_mcangle_it0.96621650
X-RAY DIFFRACTIONr_scbond_it1.8683554
X-RAY DIFFRACTIONr_scangle_it2.7844.5500
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 66 -
Rwork0.261 1425 -
obs--58.93 %

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