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- PDB-3bt5: Crystal structure of DUF305 fragment from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 3bt5
TitleCrystal structure of DUF305 fragment from Deinococcus radiodurans
ComponentsUncharacterized protein DUF305
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyDomain of unknown function DUF305, CopM-like / Domain of unknown function (DUF305) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Up-down Bundle / Mainly Alpha / DUF305 domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRamagopal, U.A. / Patskovsky, Y. / Rutter, M. / Toro, R. / Bain, K. / Meyer, A.J. / Powell, A. / Gheyi, T. / Wasserman, S. / Sauder, J.M. ...Ramagopal, U.A. / Patskovsky, Y. / Rutter, M. / Toro, R. / Bain, K. / Meyer, A.J. / Powell, A. / Gheyi, T. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of DUF305 fragment from Deinococcus radiodurans.
Authors: Ramagopal, U.A. / Patskovsky, Y. / Rutter, M. / Toro, R. / Bain, K. / Meyer, A.J. / Powell, A. / Gheyi, T. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 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: Uncharacterized protein DUF305
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7982
Polymers19,7631
Non-polymers351
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.690, 49.690, 71.191
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Uncharacterized protein DUF305


Mass: 19762.838 Da / Num. of mol.: 1 / Fragment: Residues 22-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Species: Deinococcus radiodurans / Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / Gene: DR_1099 / Plasmid: BC-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RVD0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 3M Sodium chloride, 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: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 37848 / Num. obs: 37848 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.042 / Χ2: 0.623 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.35-1.470.65537750.431100
1.4-1.457.10.47437770.449100
1.45-1.527.20.28537900.458100
1.52-1.67.20.19237950.487100
1.6-1.77.30.12937580.519100
1.7-1.837.20.09137950.538100
1.83-2.027.30.06137900.638100
2.02-2.317.30.04238010.823100
2.31-2.917.40.03638200.961100
2.91-5070.03137470.9197

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QF9

2qf9


Resolution: 1.35→25.01 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.504 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1914 5.1 %RANDOM
Rwork0.154 ---
all0.156 37810 --
obs0.156 37810 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.942 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 1 126 1409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211315
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9711788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1745176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09122.38867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48815259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1841521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021017
X-RAY DIFFRACTIONr_nbd_refined0.2230.3661
X-RAY DIFFRACTIONr_nbtor_refined0.310.5922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.519
X-RAY DIFFRACTIONr_mcbond_it4.082844
X-RAY DIFFRACTIONr_mcangle_it5.05131312
X-RAY DIFFRACTIONr_scbond_it5.3542520
X-RAY DIFFRACTIONr_scangle_it7.5083465
X-RAY DIFFRACTIONr_rigid_bond_restr3.90831364
X-RAY DIFFRACTIONr_sphericity_free16.5513127
X-RAY DIFFRACTIONr_sphericity_bonded10.14331282
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 130 -
Rwork0.242 2667 -
all-2797 -
obs--100 %

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