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- PDB-4kl7: Crystal structure of the catalytic domain of RpfB from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 4kl7
TitleCrystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis
ComponentsResuscitation-promoting factor RpfB
KeywordsHYDROLASE / cell wall hydrolase
Function / homology
Function and homology information


dormancy exit of symbiont in host / positive regulation of growth rate / 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 / G5 domain / G5 domain / G5 domain profile. / G5 / Lysozyme - #10 ...Resuscitation-promoting factor, domain of unknown function DUF348 / G5-linked-Ubiquitin-like domain / : / Resuscitation-promoting factor, core lysozyme-like domain / Transglycosylase-like domain / G5 domain / G5 domain / G5 domain profile. / G5 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Resuscitation-promoting factor RpfB / Resuscitation-promoting factor RpfB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSqueglia, F. / Romano, M. / Ruggiero, A. / Berisio, R.
CitationJournal: Biophys.J. / Year: 2013
Title: Carbohydrate Recognition by RpfB from Mycobacterium tuberculosis Unveiled by Crystallographic and Molecular Dynamics Analyses.
Authors: Squeglia, F. / Romano, M. / Ruggiero, A. / Vitagliano, L. / De Simone, A. / Berisio, R.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Resuscitation-promoting factor RpfB
B: Resuscitation-promoting factor RpfB
C: Resuscitation-promoting factor RpfB
D: Resuscitation-promoting factor RpfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3306
Polymers34,1374
Non-polymers1922
Water9,296516
1
A: Resuscitation-promoting factor RpfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6302
Polymers8,5341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Resuscitation-promoting factor RpfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6302
Polymers8,5341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Resuscitation-promoting factor RpfB


Theoretical massNumber of molelcules
Total (without water)8,5341
Polymers8,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Resuscitation-promoting factor RpfB


Theoretical massNumber of molelcules
Total (without water)8,5341
Polymers8,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.427, 51.595, 66.594
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Resuscitation-promoting factor RpfB


Mass: 8534.348 Da / Num. of mol.: 4 / Fragment: UNP residues 283-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: rv37 / Gene: rpfB, Rv1009, MT1038, MTC1237.26 / Production host: Escherichia coli (E. coli)
References: UniProt: O05594, UniProt: P9WG29*PLUS, Hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6 mg mL-1, 0,5% (w/v) PEG8000, 1M ammonium sulphate, 0,1 M Hepes, pH 7.5, and 120 mM benzamidine , 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: 1.5 Å
DetectorType: Saturn944 / Detector: CCD
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 38135 / Num. obs: 38135 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→25.327 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.347 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19221 2076 5.1 %RANDOM
Rwork0.14487 ---
obs0.14727 -82.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.39 Å2
2--1.16 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 10 516 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212464
X-RAY DIFFRACTIONr_bond_other_d0.0020.021616
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.8893360
X-RAY DIFFRACTIONr_angle_other_deg1.0883.0043836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80123.226124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48715316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8811524
X-RAY DIFFRACTIONr_chiral_restr0.1080.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
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_it1.361.51552
X-RAY DIFFRACTIONr_mcbond_other0.5461.5680
X-RAY DIFFRACTIONr_mcangle_it2.09422404
X-RAY DIFFRACTIONr_scbond_it3.0543912
X-RAY DIFFRACTIONr_scangle_it4.3874.5956
X-RAY DIFFRACTIONr_rigid_bond_restr1.49334080
X-RAY DIFFRACTIONr_sphericity_free5.6933531
X-RAY DIFFRACTIONr_sphericity_bonded2.21634018
LS refinement shellResolution: 1.451→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 114 -
Rwork0.162 2076 -
obs--61.1 %

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