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- PDB-3h9x: Crystal Structure of the PSPTO_3016 protein from Pseudomonas syri... -

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Basic information

Entry
Database: PDB / ID: 3h9x
TitleCrystal Structure of the PSPTO_3016 protein from Pseudomonas syringae, Northeast Structural Genomics Consortium Target PsR293
Componentsuncharacterized protein PSPTO_3016
Keywordsstructural genomics / unknown function / alpha-beta protein. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyAspartate Aminotransferase, domain 1 - #30 / Uncharacterised protein YjbR / YjbR-like superfamily / YjbR / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / MmcQ/YjbR family DNA-binding protein
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsSeetharaman, J. / Lew, S. / Forouhar, F. / Hamilton, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. ...Seetharaman, J. / Lew, S. / Forouhar, F. / Hamilton, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a "double wing" DNA binding motif.
Authors: Feldmann, E.A. / Seetharaman, J. / Ramelot, T.A. / Lew, S. / Zhao, L. / Hamilton, K. / Ciccosanti, C. / Xiao, R. / Acton, T.B. / Everett, J.K. / Tong, L. / Montelione, G.T. / Kennedy, M.A.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein PSPTO_3016
B: uncharacterized protein PSPTO_3016
C: uncharacterized protein PSPTO_3016
D: uncharacterized protein PSPTO_3016


Theoretical massNumber of molelcules
Total (without water)59,8824
Polymers59,8824
Non-polymers00
Water66737
1
A: uncharacterized protein PSPTO_3016


Theoretical massNumber of molelcules
Total (without water)14,9711
Polymers14,9711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein PSPTO_3016


Theoretical massNumber of molelcules
Total (without water)14,9711
Polymers14,9711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: uncharacterized protein PSPTO_3016


Theoretical massNumber of molelcules
Total (without water)14,9711
Polymers14,9711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: uncharacterized protein PSPTO_3016


Theoretical massNumber of molelcules
Total (without water)14,9711
Polymers14,9711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.302, 48.546, 68.047
Angle α, β, γ (deg.)87.070, 92.400, 93.570
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
uncharacterized protein PSPTO_3016


Mass: 14970.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: PSPTO3016, PSPTO_3016 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q880Y4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 100mM NaCitrate (pH 4.2), 20% PEG8k, and 60mM NaNO3. , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97896 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97896 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 38733 / Num. obs: 37487 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.06 / Net I/σ(I): 12.18
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.37 / Num. unique all: 3919 / Rsym value: 0.249 / % possible all: 93.5

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.51→19.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 326319.906 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2758 9.6 %RANDOM
Rwork0.21 ---
all0.213 38686 --
obs0.212 28818 74.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.721 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1--16.78 Å23.89 Å20.51 Å2
2--20.47 Å219.07 Å2
3----3.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.51→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 0 37 3921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 160 10.1 %
Rwork0.334 1427 -
obs-1587 40 %

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