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- PDB-1iyb: Crystal Structure of the Nicotiana glutinosa Ribonuclease NW -

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Basic information

Entry
Database: PDB / ID: 1iyb
TitleCrystal Structure of the Nicotiana glutinosa Ribonuclease NW
ComponentsRibonuclease
KeywordsHYDROLASE / ribonuclease
Function / homology
Function and homology information


ribonuclease T2 activity / RNA catabolic process / hydrolase activity / RNA binding / extracellular region
Similarity search - Function
Ribonuclease T2, eukaryotic / 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, eukaryotic / 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
GUANOSINE-5'-MONOPHOSPHATE / Ribonuclease NW
Similarity search - Component
Biological speciesNicotiana glutinosa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKawano, S. / Kakuta, Y. / Kimura, M.
CitationJournal: Biochemistry / Year: 2002
Title: Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallography
Authors: Kawano, S. / Kakuta, Y. / Kimura, M.
History
DepositionAug 5, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease
B: Ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9794
Polymers46,2532
Non-polymers7262
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.800, 94.300, 98.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease / ribonuclease M5


Mass: 23126.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana glutinosa (plant) / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus)
References: UniProt: Q7XZV5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium dihydrogen, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMsodium phosphate1droppH7.0
310 mM5'-GMP1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→37.43 Å / Num. obs: 62367 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3581 / % possible all: 53.8
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 37.4 Å
Reflection shell
*PLUS
% possible obs: 53.8 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
d*TREKdata scaling
d*TREKdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DIX

1dix


Resolution: 1.5→37.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 315208.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3152 5.1 %RANDOM
Rwork0.212 ---
all-62367 --
obs-62367 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.5283 Å2 / ksol: 0.386094 e/Å3
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---1.08 Å20 Å2
3---0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 48 410 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 359 5.2 %
Rwork0.244 6526 -
obs-6885 62.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION35GMP_XPLOR.PARAM
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 37.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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