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- PDB-4q4g: Structure of the Resuscitation Promoting Factor Interacting prote... -

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Basic information

Entry
Database: PDB / ID: 4q4g
TitleStructure of the Resuscitation Promoting Factor Interacting protein RipA mutated at C383
ComponentsPeptidoglycan endopeptidase RipA
KeywordsHYDROLASE / alpha-beta / cell wall 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: 0.97 Å
AuthorsBerisio, 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 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 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
X: Peptidoglycan endopeptidase RipA


Theoretical massNumber of molelcules
Total (without water)49,8291
Polymers49,8291
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.757, 65.505, 67.978
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: 49828.801 Da / Num. of mol.: 1 / Mutation: C383A
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.: 395 / 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: 5 and 8 mg mL-1 protein concentration, respectively, and 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9343 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9343 Å / Relative weight: 1
ReflectionResolution: 0.97→30 Å / Num. all: 97797 / Num. obs: 97211 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 0.97→1 Å / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.5.0110 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→10.54 Å / Cor.coef. Fo:Fc: 0.981 / SU B: 0.382 / SU ML: 0.01 / ESU R: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.17462 -5.1 %
Rwork0.12627 --
obs0.12627 93643 96.4 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.752 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 0.97→10.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 0 395 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221569
X-RAY DIFFRACTIONr_bond_other_d0.0060.021067
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.972135
X-RAY DIFFRACTIONr_angle_other_deg1.04632594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03622.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27515236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1691512
X-RAY DIFFRACTIONr_chiral_restr0.1270.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
X-RAY DIFFRACTIONr_mcbond_it1.8061.51020
X-RAY DIFFRACTIONr_mcbond_other0.8461.5427
X-RAY DIFFRACTIONr_mcangle_it2.73521635
X-RAY DIFFRACTIONr_scbond_it4.4213549
X-RAY DIFFRACTIONr_scangle_it6.2674.5500
X-RAY DIFFRACTIONr_rigid_bond_restr2.03332636
X-RAY DIFFRACTIONr_sphericity_free12.1743403
X-RAY DIFFRACTIONr_sphericity_bonded4.09832600
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.335 6308 -
Rfree-0 -
obs--89.27 %

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