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- PDB-1jy5: RNase-related protein from Calystegia sepium -

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Basic information

Entry
Database: PDB / ID: 1jy5
TitleRNase-related protein from Calystegia sepium
ComponentsCalsepRRP
KeywordsHYDROLASE / RNase / alpha-beta protein
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-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesCalystegia sepium (hedge bindweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J.M. / Peumans, W.J. / De Ranter, C.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of an RNase-related protein from Calystegia sepium.
Authors: Rabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J.
History
DepositionSep 11, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 13, 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: CalsepRRP
B: CalsepRRP


Theoretical massNumber of molelcules
Total (without water)46,7982
Polymers46,7982
Non-polymers00
Water6,756375
1
A: CalsepRRP


Theoretical massNumber of molelcules
Total (without water)23,3991
Polymers23,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CalsepRRP


Theoretical massNumber of molelcules
Total (without water)23,3991
Polymers23,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.687, 121.687, 66.059
Angle α, β, γ (deg.)90, 90, 120
Int Tables number171
Space group name H-MP62

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Components

#1: Protein CalsepRRP / RNase-like protein


Mass: 23399.148 Da / Num. of mol.: 2 / Fragment: residues 1-212 / Source method: isolated from a natural source / Source: (natural) Calystegia sepium (hedge bindweed) / References: UniProt: Q9M7C7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: NaCl, 0.1M acetate buffer, MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 M1dropNaCl
20.1 Macetate1droppH4.6
330 %MPD1drop
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 163993 / Num. obs: 140214 / % possible obs: 85.5 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Redundancy: 4.63 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 20.71
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 5.12 / Num. unique all: 1739 / Rsym value: 0.338 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 35416 / Num. measured all: 163993
Reflection shell
*PLUS
% possible obs: 66.3 % / Num. unique obs: 1739 / Num. measured obs: 7023

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DIX

1dix


Resolution: 2.05→27.63 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3486 9.953 %Random
Rwork0.207 ---
all0.211 35023 --
obs0.211 35023 99.7 %-
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å22.07 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.05→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 0 375 3519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.272 555 -
Rwork0.222 --
obs-5810 100 %
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.2074 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.2074
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor obs: 0.222

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