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- PDB-3nj2: Crystal structure of cce_0566 from the cyanobacterium Cyanothece ... -

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Basic information

Entry
Database: PDB / ID: 3nj2
TitleCrystal structure of cce_0566 from the cyanobacterium Cyanothece 51142, a protein associated with nitrogen fixation from the DUF269 family
ComponentsDUF269-containing protein
KeywordsUNKNOWN FUNCTION / cyanobacteria / circadium rhythms / nitrogen fixation
Function / homologyProtein of unknown function DUF269 / Uncharacterised protein family UPF0460 / Protein of unknown function, DUF269 / Putative cytoplasmic protein / Orthogonal Bundle / Mainly Alpha / DUF269-containing protein
Function and homology information
Biological speciesCyanothece sp. ATCC 51142 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRobinson, H. / Ralston, C.Y. / Addlagatta, A. / Buchko, G.W.
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family.
Authors: Buchko, G.W. / Robinson, H.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Sep 6, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: DUF269-containing protein
B: DUF269-containing protein


Theoretical massNumber of molelcules
Total (without water)39,4592
Polymers39,4592
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-14 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.079, 44.573, 67.724
Angle α, β, γ (deg.)90.00, 111.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DUF269-containing protein


Mass: 19729.605 Da / Num. of mol.: 2 / Fragment: UNP residues 19-171
Source method: isolated from a genetically manipulated source
Details: NdeI, BamHI site / Source: (gene. exp.) Cyanothece sp. ATCC 51142 (bacteria) / Gene: cce_0566 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1WPD5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol, protein in 100 mM NaCl, 20 mM Tris, 1 mM DTT, pH 7.1. Protein 2 mg/mL, Mix 1.5 uL of protein ...Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol, protein in 100 mM NaCl, 20 mM Tris, 1 mM DTT, pH 7.1. Protein 2 mg/mL, Mix 1.5 uL of protein and precipatant, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.59→33 Å / Num. all: 38536 / Num. obs: 38536 / % possible obs: 91.692 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.938 Å2
Reflection shellResolution: 1.593→1.634 Å / Num. unique all: 2312 / % possible all: 75.34

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G7P

3g7p


Resolution: 1.59→33 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.926 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 2057 5.1 %RANDOM
Rwork0.21 ---
obs0.2123 38536 91.69 %-
all-38536 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.764 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20.72 Å2
2---0.53 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.59→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 0 300 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.191.9663367
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.35423.565115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00415443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7191520
X-RAY DIFFRACTIONr_chiral_restr0.1430.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211856
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4231.51505
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33622434
X-RAY DIFFRACTIONr_scbond_it3.5483979
X-RAY DIFFRACTIONr_scangle_it5.5624.5933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 111 -
Rwork0.326 2312 -
obs--75.34 %

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