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- PDB-2bti: Structure-function studies of the RmsA CsrA post-transcriptional ... -

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Basic information

Entry
Database: PDB / ID: 2bti
TitleStructure-function studies of the RmsA CsrA post-transcriptional global regulator protein family reveals a class of RNA-binding structure
ComponentsCARBON STORAGE REGULATOR HOMOLOG
KeywordsRNA BINDING PROTEIN / RMSA / CSRA
Function / homology
Function and homology information


regulation of carbohydrate metabolic process / mRNA catabolic process / positive regulation of translational initiation / negative regulation of translational initiation / mRNA 5'-UTR binding / cytoplasm
Similarity search - Function
Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family
Similarity search - Domain/homology
ACETATE ION / Translational regulator CsrA
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHeeb, S. / Kuehne, S.A. / Bycroft, M. / Crivii, S. / Allen, M.D. / Haas, D. / Camara, M. / Williams, P.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Functional Analysis of the Post-Transcriptional Regulator Rsma Reveals a Novel RNA-Binding Site.
Authors: Heeb, S. / Kuehne, S.A. / Bycroft, M. / Crivii, S. / Allen, M.D. / Haas, D. / Camara, M. / Williams, P.
History
DepositionMay 31, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBON STORAGE REGULATOR HOMOLOG
B: CARBON STORAGE REGULATOR HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3274
Polymers14,1722
Non-polymers1552
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.573, 37.573, 186.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein CARBON STORAGE REGULATOR HOMOLOG


Mass: 7085.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A1JK11*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GENOMIC SEQUENCE FOR THIS ORGANISM ARE NOT YET PUBLISHED OR IN THE NCBI DATABASES, BUT CAN BE ...THE GENOMIC SEQUENCE FOR THIS ORGANISM ARE NOT YET PUBLISHED OR IN THE NCBI DATABASES, BUT CAN BE RETRIEVED FROM THE SANGER INSTITUTE. HTTP://WWW.SANGER.AC.UK/PROJECTS/Y_ENTEROCOLITICA/

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 48 %
Crystal growpH: 4.6
Details: 0.16M AMMONIUM SULPHATE, 0.08M SODIUM ACETATE PH 4.6, 20% PEG 4000, 20% GLYCEROL, 10 MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→26.5 Å / Num. obs: 9675 / % possible obs: 98.4 % / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→100 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 4.6
RfactorNum. reflection% reflectionSelection details
Rfree0.254 497 5.1 %RANDOM
Rwork0.224 ---
obs0.224 9632 98.1 %-
Solvent computationBsol: 48.383 Å2 / ksol: 0.383018 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.674 Å20 Å20 Å2
2---5.674 Å20 Å2
3---11.348 Å2
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 9 44 948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.457
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.1 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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