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- PDB-3ne0: Structure and functional regulation of RipA, a mycobacterial enzy... -

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Basic information

Entry
Database: PDB / ID: 3ne0
TitleStructure and functional regulation of RipA, a mycobacterial enzyme essential for daughter cell separation
ComponentsResuscitation promoting factor Interacting Protein A
KeywordsHYDROLASE / cell wall / peptidoglycan / tuberculosis
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 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / 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 / MAD / Resolution: 1 Å
AuthorsRuggiero, A. / Squeglia, F. / Berisio, R.
CitationJournal: Structure / Year: 2010
Title: Structure and Functional Regulation of RipA, a Mycobacterial Enzyme Essential for Daughter Cell Separation.
Authors: Ruggiero, A. / Marasco, D. / Squeglia, F. / Soldini, S. / Pedone, E. / Pedone, C. / Berisio, R.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Resuscitation promoting factor Interacting Protein A


Theoretical massNumber of molelcules
Total (without water)22,5521
Polymers22,5521
Non-polymers00
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.866, 65.560, 67.931
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 Resuscitation promoting factor Interacting Protein A / INVASION PROTEIN


Mass: 22551.629 Da / Num. of mol.: 1 / Fragment: UNP residues 263-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: h37rv / Gene: rv1477 / Production host: Escherichia coli (E. coli) / References: UniProt: O53168
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 32.42 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: 8% (v/v) 2-Propanol, 16% (w/v) PEG4000, 60 mM Sodium citrate trihydrate buffer, pH 5.6, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9737, 0.9785, 0.9787, 0.9737
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 30, 2008 / Details: mirrors
RadiationMonochromator: Si(111) monochromator. / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97371
20.97851
30.97871
ReflectionResolution: 1→30 Å / Num. all: 88997 / Num. obs: 85882 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3 / % possible all: 72.6

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Processing

Software
NameClassification
HKL-2000data collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1→10 Å / Num. parameters: 17484 / Num. restraintsaints: 7222 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.137 4295 -RANDOM
Rwork0.104 ---
obs0.1055 81445 91.7 %-
all-81445 --
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 1526 / Occupancy sum non hydrogen: 1934
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 0 390 1933
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0296
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.117
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0.103
LS refinement shellResolution: 1→1.04 Å /
RfactorNum. reflection
Rfree0.15 347
Rwork0.13 -
obs-7021

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