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- PDB-2ea1: Crystal structure of Ribonuclease I from Escherichia coli COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 2ea1
TitleCrystal structure of Ribonuclease I from Escherichia coli COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE
ComponentsRibonuclease I
KeywordsHYDROLASE / PROTEIN-GPG COMPLEX
Function / homology
Function and homology information


Enterobacter ribonuclease / Enterobacter ribonuclease activity / ribonuclease T2 activity / RNA catabolic process / outer membrane-bounded periplasmic space / RNA binding / 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
GUANYLYL-2',5'-PHOSPHOGUANOSINE / Ribonuclease I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhou, K. / Pan, J. / Padmanabhan, S. / Lim, R.W. / Lim, L.W.
Citation
Journal: To be Published
Title: Crystal Structure of Ribonuclease I from Escherichia Coli Complexed with Guanylyl-2(Prime),5(Prime)-Guanosine at 1.80 Angstroms Resolution
Authors: Zhou, K. / Pan, J. / Padmanabhan, S. / Lim, R.W. / Lim, L.W.
#1: Journal: Arch.Biochem.Biophys. / Year: 2001
Title: Overexpression, Biophysical Characterization, and Crystallization of Ribonuclease I from Escherichia Coli, a Broad-Specificity Enzyme in the Rnase T2 Family
Authors: Padmanabhan, S. / Zhou, K. / Chu, C.Y. / Lim, R.W. / Lim, L.W.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Three-dimensional structure of ribonuclease T1 complexed with guanylyl-2',5'-guanosine at 1.8 A resolution
Authors: Koepke, J. / Maslowska, M. / Heinemann, U. / Saenger, W.
History
DepositionJan 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8212
Polymers27,1931
Non-polymers6281
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.200, 49.870, 54.520
Angle α, β, γ (deg.)90.00, 96.37, 90.00
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) / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21LYSS / References: UniProt: P21338, EC: 3.1.27.6
#2: Chemical ChemComp-GPG / GUANYLYL-2',5'-PHOSPHOGUANOSINE


Mass: 628.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N10O12P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 25% PEG 3350, 0.1M MES, 0.1M AMMONIUM ACETATE, 1MM MAGNESIUM CHLORIDE, 10% GLYCEROL, 4MM EDTA, VAPOR DIFFUSION, HANGING DROP, pH 6.10, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 12, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→54.23 Å / Num. all: 18458 / Num. obs: 18428 / % possible obs: 85.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.182 / % possible all: 36.4

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→54.23 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.234 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 957 5.2 %RANDOM
Rwork0.218 ---
all0.231 18428 --
obs0.22 17471 85.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20.26 Å2
2---1.19 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 43 142 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222005
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9792721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06323.40494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50415323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5491517
X-RAY DIFFRACTIONr_chiral_restr0.170.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021559
X-RAY DIFFRACTIONr_nbd_refined0.2270.2960
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.213
X-RAY DIFFRACTIONr_mcbond_it1.2681.51244
X-RAY DIFFRACTIONr_mcangle_it2.09621941
X-RAY DIFFRACTIONr_scbond_it3.2633889
X-RAY DIFFRACTIONr_scangle_it4.4084.5780
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 30 -
Rwork0.263 527 -
obs--35.08 %

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