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- PDB-3i3u: Crystal structure of lp_1913 protein from lactobacillus plantarum... -

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Basic information

Entry
Database: PDB / ID: 3i3u
TitleCrystal structure of lp_1913 protein from lactobacillus plantarum, northeast structural genomics Consortium target lpr140a
Componentsuncharacterized protein lp_1913
Keywordsstructural genomics / unknown function / LACTOBACILLUS PLANTARUM / LP_1913 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Rhodanese domain-containing protein / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSeetharaman, J. / Chen, Y. / Forouhar, F. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Chen, Y. / Forouhar, F. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / 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 lp_1913 protein from lactobacillus plantarum, northeast structural genomics Consortium target lpr140a
Authors: Seetharaman, J. / Chen, Y. / Forouhar, F. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein lp_1913
B: uncharacterized protein lp_1913
C: uncharacterized protein lp_1913
D: uncharacterized protein lp_1913
E: uncharacterized protein lp_1913
F: uncharacterized protein lp_1913


Theoretical massNumber of molelcules
Total (without water)73,9486
Polymers73,9486
Non-polymers00
Water90150
1
A: uncharacterized protein lp_1913
B: uncharacterized protein lp_1913
C: uncharacterized protein lp_1913


Theoretical massNumber of molelcules
Total (without water)36,9743
Polymers36,9743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-34 kcal/mol
Surface area13890 Å2
MethodPISA
2
D: uncharacterized protein lp_1913
E: uncharacterized protein lp_1913
F: uncharacterized protein lp_1913


Theoretical massNumber of molelcules
Total (without water)36,9743
Polymers36,9743
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-35 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.706, 60.287, 60.319
Angle α, β, γ (deg.)120.04, 89.96, 90.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
uncharacterized protein lp_1913


Mass: 12324.717 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: lp_1913 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88VW8, UniProt: F9UPN6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.86 Å3/Da / Density % sol: 33.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaBr 0.1M, MES 0.1M, PEG 8000 20%, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 36176 / Num. obs: 36176 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 0.1 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.035 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.213 / Num. unique all: 3389 / Rsym value: 0.198 / % possible all: 91

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→26.12 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 92884.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1206 4.9 %RANDOM
Rwork0.264 ---
obs0.264 24788 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.9606 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.37 Å2-1.03 Å2-3.33 Å2
2---1.44 Å2-0.98 Å2
3----2.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.8→26.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 0 50 3972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.71
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 163 4.3 %
Rwork0.267 3617 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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