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- PDB-2nvo: Crystal structure of Deinococcus radiodurans RO (RSR) protein -

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Basic information

Entry
Database: PDB / ID: 2nvo
TitleCrystal structure of Deinococcus radiodurans RO (RSR) protein
ComponentsRo sixty-related protein, RSR
KeywordsRNA BINDING PROTEIN / alpha helical repeats / von Willebrand Factor A domain / beta-sheet
Function / homology
Function and homology information


ribonucleoprotein complex / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
TROVE domain / TROVE domain superfamily / RNA-binding protein RO60 / TROVE domain / TROVE domain profile. / von Willebrand factor, type A domain / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
60 kDa SS-A/Ro ribonucleoprotein homolog
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsRamesh, A. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of Rsr, an ortholog of the antigenic Ro protein, links conformational flexibility to RNA binding activity.
Authors: Ramesh, A. / Savva, C.G. / Holzenburg, A. / Sacchettini, J.C.
History
DepositionNov 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE According to authors, residue 433 is a valine. The conflict with the database could be due ...SEQUENCE According to authors, residue 433 is a valine. The conflict with the database could be due to an error in the database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ro sixty-related protein, RSR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8942
Polymers57,8541
Non-polymers401
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Ro sixty-related protein, RSR
hetero molecules

A: Ro sixty-related protein, RSR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7884
Polymers115,7082
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area1440 Å2
ΔGint-32 kcal/mol
Surface area43130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.556, 87.610, 70.623
Angle α, β, γ (deg.)90.00, 96.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-534-

HOH

21A-547-

HOH

31A-551-

HOH

41A-638-

HOH

51A-829-

HOH

61A-839-

HOH

71A-849-

HOH

81A-851-

HOH

91A-875-

HOH

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Components

#1: Protein Ro sixty-related protein, RSR / 60 kDa SS-A/Ro ribonucleoprotein homolog


Mass: 57854.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: rsr / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RUW8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1Mimidazole, 12% PEG 8000,0.2M calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934, 0.97926, 0.97939, 0.94927
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979261
30.979391
40.949271
ReflectionResolution: 1.89→46.6 Å / Num. all: 48814 / Num. obs: 48610 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Biso Wilson estimate: 34.46 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.64 / Num. unique all: 4243 / % possible all: 85.3

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Processing

Software
NameClassification
MAR345data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.89→46.6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2460 -random
Rwork0.223 ---
all0.223 48610 --
obs0.223 48610 100 %-
Displacement parametersBiso mean: 25.6 Å2
Refinement stepCycle: LAST / Resolution: 1.89→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 1 401 4141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.71
X-RAY DIFFRACTIONf_bond_d0.005
LS refinement shellResolution: 1.89→1.93 Å
RfactorNum. reflection% reflection
Rfree0.49 100 -
Rwork0.42 --
obs-1974 80 %

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