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- PDB-5e27: The structure of Resuscitation Promoting Factor B from M. tubercu... -

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Basic information

Entry
Database: PDB / ID: 5.0E+27
TitleThe structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains
ComponentsResuscitation-promoting factor RpfB
KeywordsCELL ADHESION / cell wall / peptidoglycan / tuberculosis
Function / homology
Function and homology information


dormancy exit of symbiont in host / Hydrolases / quorum sensing / regulation of cell population proliferation / hydrolase activity / negative regulation of gene expression / positive regulation of gene expression / extracellular region / plasma membrane
Similarity search - Function
Resuscitation-promoting factor, domain of unknown function DUF348 / G5-linked-Ubiquitin-like domain / Resuscitation-promoting factor, core lysozyme-like domain / : / Transglycosylase-like domain / Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / G5 domain / G5 domain / G5 domain profile. ...Resuscitation-promoting factor, domain of unknown function DUF348 / G5-linked-Ubiquitin-like domain / Resuscitation-promoting factor, core lysozyme-like domain / : / Transglycosylase-like domain / Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / G5 domain / G5 domain / G5 domain profile. / G5 / Single Sheet / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Resuscitation-promoting factor RpfB / Resuscitation-promoting factor RpfB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsRuggiero, A. / Squeglia, F. / Romano, M. / Vitagliano, L. / De Simone, A. / Berisio, R.
Funding support1items
OrganizationGrant numberCountry
EUGA 609535
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains.
Authors: Ruggiero, A. / Squeglia, F. / Romano, M. / Vitagliano, L. / De Simone, A. / Berisio, R.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Resuscitation-promoting factor RpfB
B: Resuscitation-promoting factor RpfB


Theoretical massNumber of molelcules
Total (without water)51,8072
Polymers51,8072
Non-polymers00
Water1,36976
1
A: Resuscitation-promoting factor RpfB


Theoretical massNumber of molelcules
Total (without water)25,9031
Polymers25,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Resuscitation-promoting factor RpfB


Theoretical massNumber of molelcules
Total (without water)25,9031
Polymers25,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.376, 126.990, 86.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Resuscitation-promoting factor RpfB / Resuscitation-promoting factor rpfB


Mass: 25903.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: rpfB, ABI38_15460, BN1303_02209, ERS024750_01702, ERS024751_02059, ERS024758_02236, ERS024764_01503, ERS094182_03333, ERS124362_01696, ERS124821_03131, ERS124823_03398, ERS124824_03090, ...Gene: rpfB, ABI38_15460, BN1303_02209, ERS024750_01702, ERS024751_02059, ERS024758_02236, ERS024764_01503, ERS094182_03333, ERS124362_01696, ERS124821_03131, ERS124823_03398, ERS124824_03090, ERS124825_03322, ERS124826_03034, ERS124827_03238, ERS124828_02982, ERS124829_03081, ERS124830_03164, ERS124832_03150, IQ42_14370, IQ45_14195, IQ47_14175, IQ48_14250, IU12_14990, IU13_14360, IU15_14665, IU16_14305, IU21_14520, T209_14145
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045K816, UniProt: P9WG29*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 5 mg mL-1 protein, 18 % (v/v) ethanol in 50 mM sodium Tris-HCl buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.94,0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.941
20.971
ReflectionResolution: 2.6→50 Å / Num. obs: 17505 / % possible obs: 93.7 % / Redundancy: 16.2 % / Net I/σ(I): 31.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.889 / SU B: 31.924 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.797 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29106 826 5.1 %RANDOM
Rwork0.22181 ---
obs0.22546 15476 92.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: 1 / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 0 76 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223385
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.9524644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0285448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78924.126143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.77315490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5211529
X-RAY DIFFRACTIONr_chiral_restr0.1380.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222646
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6551.52222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24123588
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94731163
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3794.51055
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.665 Å
RfactorNum. reflection% reflection
Rfree0.31 49 -
Rwork0.32 733 -
obs--63.63 %

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