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- PDB-4emn: Crystal structure of RpfB catalytic domain in complex with benzamidine -

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Basic information

Entry
Database: PDB / ID: 4emn
TitleCrystal structure of RpfB catalytic domain in complex with benzamidine
ComponentsProbable resuscitation-promoting factor rpfB
KeywordsHYDROLASE / alpha beta
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
BENZAMIDINE / Resuscitation-promoting factor RpfB / Resuscitation-promoting factor RpfB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsRuggiero, A. / Marchant, J. / Squeglia, F. / Makarov, V. / De Simone, A. / Berisio, R.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2013
Title: Molecular determinants of inactivation of the resuscitation promoting factor B from Mycobacterium tuberculosis.
Authors: Ruggiero, A. / Marchant, J. / Squeglia, F. / Makarov, V. / De Simone, A. / Berisio, R.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable resuscitation-promoting factor rpfB
B: Probable resuscitation-promoting factor rpfB
C: Probable resuscitation-promoting factor rpfB
D: Probable resuscitation-promoting factor rpfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,27912
Polymers34,3664
Non-polymers9138
Water10,215567
1
A: Probable resuscitation-promoting factor rpfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9284
Polymers8,5911
Non-polymers3363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable resuscitation-promoting factor rpfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9284
Polymers8,5911
Non-polymers3363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Probable resuscitation-promoting factor rpfB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8323
Polymers8,5911
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Probable resuscitation-promoting factor rpfB


Theoretical massNumber of molelcules
Total (without water)8,5911
Polymers8,5911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.545, 50.733, 66.421
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable resuscitation-promoting factor rpfB


Mass: 8591.399 Da / Num. of mol.: 4 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1038, rpfB, Rv1009 / Production host: Escherichia coli (E. coli) / References: UniProt: O05594, UniProt: P9WG29*PLUS
#2: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.5% peg8000, 1M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→30 Å / Num. obs: 85254 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.17→1.21 Å / Rmerge(I) obs: 0.021 / % possible all: 75.1

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Processing

Software
NameClassification
HKL-2000data collection
PHASESphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3eo5

3eo5


Resolution: 1.17→15 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1876 4263 random
Rwork0.127 --
all0.1503 --
obs0.1291 80945 -
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.17→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 64 567 3033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d0.03
LS refinement shellResolution: 1.17→1.21 Å
RfactorNum. reflection
Rfree0.018 4263
Rwork0.012 -
obs-80945

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