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- PDB-4kji: Novel re-arrangement of an RsmA/cSRa family protein to create a s... -

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Basic information

Entry
Database: PDB / ID: 4kji
TitleNovel re-arrangement of an RsmA/cSRa family protein to create a structurally distinct new RNA-binding family member
Components
  • RsmN, a RNA-binding protein of Regulator of Secondary Metabolism
  • RsmZ-2
KeywordsRNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / BETA BARREL / BETA-BARREL / POST-TRANSCRIPTIONAL REGULATION / RNA BINDING / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of carbohydrate metabolic process / mRNA catabolic process / RNA binding / identical protein binding
Similarity search - Function
Translational regulator CsrA / Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Carbon storage regulator / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, C.
CitationJournal: Structure / Year: 2013
Title: Structural Rearrangement in an RsmA/CsrA Ortholog of Pseudomonas aeruginosa Creates a Dimeric RNA-Binding Protein, RsmN.
Authors: Morris, E.R. / Hall, G. / Li, C. / Heeb, S. / Kulkarni, R.V. / Lovelock, L. / Silistre, H. / Messina, M. / Camara, M. / Emsley, J. / Williams, P. / Searle, M.S.
History
DepositionMay 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: RsmN, a RNA-binding protein of Regulator of Secondary Metabolism
B: RsmN, a RNA-binding protein of Regulator of Secondary Metabolism
C: RsmZ-2
D: RsmZ-2


Theoretical massNumber of molelcules
Total (without water)27,9194
Polymers27,9194
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.649, 83.649, 94.239
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 RsmN, a RNA-binding protein of Regulator of Secondary Metabolism


Mass: 8768.108 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA14_68470, rsmN / Plasmid: pME600 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q02EI1, UniProt: A0A0H2ZIZ8*PLUS
#2: RNA chain RsmZ-2


Mass: 5191.176 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in Pseudomonas aeruginosa

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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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growMethod: evaporation / pH: 4.5
Details: 0.08M Mg(OAc)2, 0.1M NaOAc pH 4.5, 4% benzamidine HCl, 4% PEG 8000., EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.2→29.57 Å / Num. obs: 5917 / Redundancy: 8.8 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 18.6

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Processing

Software
NameVersionClassification
DNAdata collection
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1vpz for protein and 2JPP for RNA

1vpz

2jpp


Resolution: 3.2→29.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 29.686 / SU ML: 0.464 / Cross valid method: THROUGHOUT / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.317 267 4.5 %RANDOM
Rwork0.222 ---
obs0.226 5628 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 109.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.99 Å20 Å20 Å2
2--3.99 Å20 Å2
3----7.98 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 688 0 0 1696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0161784
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.7442561
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87222.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.85115200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7881516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021080
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 14 -
Rwork0.372 330 -
obs--96.36 %

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