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- PDB-2pqx: E. coli RNase 1 (in vivo folded) -

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Basic information

Entry
Database: PDB / ID: 2pqx
TitleE. coli RNase 1 (in vivo folded)
ComponentsRibonuclease I
KeywordsHYDROLASE / ribonuclease
Function / homology
Function and homology information


Enterobacter ribonuclease / Enterobacter ribonuclease activity / ribonuclease T2 activity / RNA catabolic process / outer membrane-bounded periplasmic space / RNA binding / extracellular region / cytoplasm
Similarity search - Function
Ribonuclease T2, prokaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily ...Ribonuclease T2, prokaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsMessens, J. / Loris, R. / Wyns, L.
CitationJournal: To be Published
Title: Crystal structure of E. coli ribonuclease 1
Authors: Messens, J. / Collet, J.F. / Loris, R. / Wyns, L.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4283
Polymers27,1931
Non-polymers2352
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.894, 49.626, 53.398
Angle α, β, γ (deg.)90.000, 96.863, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease I / Enterobacter ribonuclease / RNase I


Mass: 27192.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rna, rnsA / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl 21(DE3) PlysS / References: UniProt: P21338, EC: 3.1.27.6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1 M MES pH 6.1, 0.1 M NH4AC, 10 % glycerol, 1 mM MgCl2, and 25 % polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.42→15 Å / Num. all: 39060 / Num. obs: 39060 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.051 / Net I/σ(I): 15.75
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.95 / Num. unique all: 3858 / Rsym value: 0.344 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.42→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3168 -random
Rwork0.188 ---
all-39060 --
obs-39060 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.42→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 13 219 2095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.554

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