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- PDB-3c9g: Crystal structure of uncharacterized UPF0201 protein AF_135 -

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Basic information

Entry
Database: PDB / ID: 3c9g
TitleCrystal structure of uncharacterized UPF0201 protein AF_135
ComponentsUPF0200/UPF0201 protein AF_1395
KeywordsNUCLEOTIDE BINDING PROTEIN / uncharacterized UPF0201 protein AF_135 / Structural genomics / PSI-II / dimer / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


Nucleoside triphosphate hydrolase-related / Uncharacterised protein family UPF0201 / RNA binding / AAA domain / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0200/UPF0201 protein AF_1395
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSugadev, R. / Ozyurt, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized UPF0201 protein AF_135.
Authors: Sugadev, R. / Ozyurt, S. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0200/UPF0201 protein AF_1395
B: UPF0200/UPF0201 protein AF_1395


Theoretical massNumber of molelcules
Total (without water)32,8962
Polymers32,8962
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.986, 79.986, 95.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UPF0200/UPF0201 protein AF_1395


Mass: 16447.885 Da / Num. of mol.: 2 / Fragment: Residues 183-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM 4304 / VC-16 / JCM 9628 / NBRC 100126 / Gene: AF_1395 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O28876
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1 M Sodium citrate pH 5.2, 30% PEG 4000, 0.1M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2006 / Details: SGX_CAT
RadiationMonochromator: SGX_CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 25121 / Num. obs: 25121 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NWU

2nwu


Resolution: 2.3→24.45 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 147025.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of ...Details: The Friedel pairs were used in phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines. The R free value is slightly higher.
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1087 4.9 %RANDOM
Rwork0.269 ---
obs0.269 22409 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7094 Å2 / ksol: 0.315086 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.12 Å20 Å20 Å2
2--6.12 Å20 Å2
3----12.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 0 20 2109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 118 4.2 %
Rwork0.306 2708 -
obs--64.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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