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- PDB-2nrq: Crystal structure of protein SSO0741 from Sulfolobus solfataricus... -

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Basic information

Entry
Database: PDB / ID: 2nrq
TitleCrystal structure of protein SSO0741 from Sulfolobus solfataricus, Pfam DUF54
ComponentsHypothetical protein ORF-c20_032
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / Sulfolobus solfataricus / 10077c / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyUncharacterised protein family UPF0201 / RNA binding / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta / RNA-binding protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsRao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Plos One / Year: 2008
Title: UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Hypothetical protein ORF-c20_032


Theoretical massNumber of molelcules
Total (without water)18,7491
Polymers18,7491
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.540, 127.540, 61.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hypothetical protein ORF-c20_032


Mass: 18749.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ORF-c20_032 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UXC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium Formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 6695 / Num. obs: 6695 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→27.43 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 173184.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: the missing residues listed in Remark 465 are due to lack of electron density; Residues with missing atoms as listed in Remark 470 were modeled as ALA because of lack of electron density for side chain atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.303 234 4.1 %RANDOM
Rwork0.245 ---
obs0.245 5642 93.7 %-
all-5906 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5155 Å2 / ksol: 0.346215 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.07 Å211.44 Å20 Å2
2--4.07 Å20 Å2
3----8.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 0 17 1117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 36 4.3 %
Rwork0.287 801 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4
X-RAY DIFFRACTION5

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