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- PDB-1q5x: Structure of OF RRAA (MENG), a protein inhibitor of RNA processing -

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Basic information

Entry
Database: PDB / ID: 1q5x
TitleStructure of OF RRAA (MENG), a protein inhibitor of RNA processing
ComponentsREGULATOR OF RNASE E ACTIVITY A
Keywordshydrolase inhibitor / 3-LAYER SANDWICH / ALPHA-BETA STRUCTURE / PARALLEL BETA SHEET / ANTIPARALLEL BETA SHEET
Function / homology
Function and homology information


negative regulation of RNA catabolic process / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / ribonuclease inhibitor activity / oxaloacetate decarboxylase activity / protein homotrimerization / endoribonuclease inhibitor activity / enzyme binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Regulator of ribonuclease activity A, gammaproteobacteria / Regulator of ribonuclease activity A / Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulator of ribonuclease activity A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2 Å
AuthorsMonzingo, A.F. / Gao, J. / Qiu, J. / Georgiou, G. / Robertus, J.D.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The X-ray Structure of Escherichia coli RraA (MenG), A Protein Inhibitor of RNA Processing.
Authors: Monzingo, A.F. / Gao, J. / Qiu, J. / Georgiou, G. / Robertus, J.D.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: RraA: a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli.
Authors: LEE, K. / ZHAN, X. / GAO, J. / QIU, J. / FANG, Y. / MEGANATHAN, R. / COHEN, S.N. / GEORGIOU, G.
History
DepositionAug 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND THE AUTHOR MAINTAINS THAT THIS PROTEIN HAS BEEN MISANNOTATED IN THE SWISSPROT DATABASE. ...COMPOUND THE AUTHOR MAINTAINS THAT THIS PROTEIN HAS BEEN MISANNOTATED IN THE SWISSPROT DATABASE. THERE IS NO BIOCHEMICAL EVIDENCE THAT THE MENG GENE PRODUCT IS AN S-ADENOSYLMETHIONINE:2-DEMETHYLMENAQUINONE METHYLTRANSFERASE. HOWEVER, THERE IS NOW BIOCHEMICAL EVIDENCE SHOWING THAT THE PROTEIN BINDS RNASE E AND INHIBITS ITS ACTIVITY AS DISCUSSED IN REFERENCE 1.
Remark 700SHEET SHEET RECORDS IN THIS FILE WERE PROVIDED BY THE AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATOR OF RNASE E ACTIVITY A
B: REGULATOR OF RNASE E ACTIVITY A
C: REGULATOR OF RNASE E ACTIVITY A


Theoretical massNumber of molelcules
Total (without water)52,1143
Polymers52,1143
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-17 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.454, 93.945, 67.949
Angle α, β, γ (deg.)90.00, 132.72, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE BIOLOGICAL UNIT IS THE HOMOTRIMER CONTAINED IN THE ASYMMETRIC UNIT

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Components

#1: Protein REGULATOR OF RNASE E ACTIVITY A / RRAA / S-ADENOSYLMETHIONINE:2-DEMETHYLMENAQUINONE METHYLTRANSFERASE / MENG


Mass: 17371.264 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MENG / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8R0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: AMMONIUM PHOSPHATE, SODIUM CITRATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.8 Mammonium phosphate1reservoir
20.1 Msodium citrate1reservoirpH5.2

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 9, 2001
RadiationMonochromator: DOUBLE FOCUSSING MIRRORS (NI & PT) + NI FILTER
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 28089 / Num. obs: 28089 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.328 / % possible all: 71.8
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 2.9 %
Reflection shell
*PLUS
% possible obs: 71.8 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 1334 RANDOM
Rwork0.226 --
all0.228 26489 -
obs0.228 26489 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 0 244 3817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.242
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.246

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