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- PDB-3fnj: Crystal structure of the full-length lp_1913 protein from Lactoba... -

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Basic information

Entry
Database: PDB / ID: 3fnj
TitleCrystal structure of the full-length lp_1913 protein from Lactobacillus plantarum, Northeast Structural Genomics Consortium Target LpR140
Componentsprotein lp_1913
Keywordsstructural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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: 2.7 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 the full-length lp_1913 protein from Lactobacillus plantarum, Northeast Structural Genomics Consortium Target LpR140
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
DepositionDec 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 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: protein lp_1913
B: protein lp_1913
C: protein lp_1913
D: protein lp_1913
E: protein lp_1913
F: protein lp_1913


Theoretical massNumber of molelcules
Total (without water)87,2466
Polymers87,2466
Non-polymers00
Water1,47782
1
A: protein lp_1913
B: protein lp_1913
C: protein lp_1913


Theoretical massNumber of molelcules
Total (without water)43,6233
Polymers43,6233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-43 kcal/mol
Surface area16790 Å2
MethodPISA
2
D: protein lp_1913
E: protein lp_1913
F: protein lp_1913


Theoretical massNumber of molelcules
Total (without water)43,6233
Polymers43,6233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-42 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.365, 119.365, 67.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Detailstrimer

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Components

#1: Protein
protein lp_1913


Mass: 14541.033 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: lp_1913 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q88VW8, UniProt: F9UPN6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM Bis-Tris Propane (pH 7.0) and 1880 mM sodium thiosulfate. , Microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 51670 / Num. obs: 51464 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.06 / Net I/σ(I): 26.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 4.4 / Num. unique all: 5103 / Rsym value: 0.273 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 385035.69 / 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
Rfree0.276 1680 5 %RANDOM
Rwork0.231 ---
all0.232 51297 --
obs0.231 33497 65.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.0696 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 55.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.53 Å20 Å20 Å2
2--5.53 Å20 Å2
3----11.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 0 82 5614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.317 136 5.6 %
Rwork0.262 2281 -
obs-2281 47.1 %

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