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- PDB-3bz6: Crystal structure of a conserved protein of unknown function from... -

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Basic information

Entry
Database: PDB / ID: 3bz6
TitleCrystal structure of a conserved protein of unknown function from Pseudomonas syringae pv. tomato str. DC3000
ComponentsUPF0502 protein PSPTO_2686
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC84902 / conserved domain / Pseudomonas syringae pv. tomato str. DC3000 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF480 / Protein of unknown function, DUF480 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / UPF0502 protein PSPTO_2686
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsTan, K. / Duggan, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved protein of unknown function from Pseudomonas syringae pv. tomato str. DC3000.
Authors: Tan, K. / Duggan, E. / Clancy, S. / Joachimiak, A.
History
DepositionJan 17, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 5, 2008ID: 2NR3
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0502 protein PSPTO_2686


Theoretical massNumber of molelcules
Total (without water)20,5331
Polymers20,5331
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.025, 72.025, 73.119
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. IT IS LIKELY A MONOMER.

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Components

#1: Protein UPF0502 protein PSPTO_2686


Mass: 20532.506 Da / Num. of mol.: 1 / Fragment: Residues 1-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO_2686 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q882E2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate, 20% Isopropanol, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97943
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979431
ReflectionResolution: 2.2→31.54 Å / Num. all: 10229 / Num. obs: 10229 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 46
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.59 / Num. unique all: 426 / % possible all: 58.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.21→31.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 17.474 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.252 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24085 492 4.8 %RANDOM
Rwork0.19574 ---
all0.19788 9680 --
obs0.19788 9680 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.166 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.21→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 0 26 1342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211331
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9861801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29724.15465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96215248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2551515
X-RAY DIFFRACTIONr_chiral_restr0.1140.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2574
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2905
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4162862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24731345
X-RAY DIFFRACTIONr_scbond_it1.2932515
X-RAY DIFFRACTIONr_scangle_it1.8653456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 23 -
Rwork0.318 454 -
obs-477 58.96 %
Refinement TLS params.Method: refined / Origin x: -9.385 Å / Origin y: 32.111 Å / Origin z: 6.325 Å
111213212223313233
T-0.2744 Å2-0.0241 Å20.0066 Å2--0.3008 Å20.0163 Å2--0.0356 Å2
L5.2695 °20.3501 °21.2784 °2-2.4448 °21.978 °2--5.6473 °2
S0.0817 Å °-0.1377 Å °0.059 Å °-0.0383 Å °-0.1175 Å °0.1038 Å °0.1379 Å °0.2373 Å °0.0358 Å °

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