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- PDB-3ggn: Crystal structure of DR_A0006 from Deinococcus radiodurans. North... -

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Basic information

Entry
Database: PDB / ID: 3ggn
TitleCrystal structure of DR_A0006 from Deinococcus radiodurans. Northeast Structural Genomics Consortium Target DrR147D
ComponentsUncharacterized protein DR_A0006
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Deinococcus radiodurans / DR_A0006 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology: / Coenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Coenzyme Q-binding protein COQ10 START domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeetharaman, J. / Neely, H. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Neely, H. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of DR_A0006 from Deinococcus radiodurans.
Authors: Seetharaman, J. / Neely, H. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein DR_A0006
B: Uncharacterized protein DR_A0006


Theoretical massNumber of molelcules
Total (without water)34,8182
Polymers34,8182
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein DR_A0006


Theoretical massNumber of molelcules
Total (without water)17,4091
Polymers17,4091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Uncharacterized protein DR_A0006


Theoretical massNumber of molelcules
Total (without water)17,4091
Polymers17,4091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.498, 56.286, 51.277
Angle α, β, γ (deg.)90.00, 106.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein DR_A0006


Mass: 17408.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / Gene: DR_A0006 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RZE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6
Details: 0.1M KH2PO4, 0.1M MES pH 6.0, 40% PEG 4000, MICROBATCH UNDER OIL, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 35348 / Num. obs: 35348 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.063 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.319 / Rsym value: 0.28 / % possible all: 96.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→37.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 119679.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1674 5.1 %RANDOM
Rwork0.242 ---
obs0.242 32864 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3031 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å23.13 Å2
2--2.68 Å20 Å2
3----2.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 129 2130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 261 4.9 %
Rwork0.245 5047 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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