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- PDB-3cq9: Crystal structure of the lp_1622 protein from Lactobacillus plant... -

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Basic information

Entry
Database: PDB / ID: 3cq9
TitleCrystal structure of the lp_1622 protein from Lactobacillus plantarum. Northeast Structural Genomics Consortium target LpR114
ComponentsUncharacterized protein lp_1622
KeywordsTRANSFERASE / Q88WK7_LACPL / THIAMINE PYROPHOSPHOKINASE / NESG / LPR114 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


thiamine diphosphokinase / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / thiamine diphosphate biosynthetic process / kinase activity / ATP binding
Similarity search - Function
Thiamin pyrophosphokinase / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiamin pyrophosphokinase / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Maglaqui, M. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Maglaqui, M. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the lp_1622 protein from Lactobacillus plantarum.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Maglaqui, M. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein lp_1622
B: Uncharacterized protein lp_1622
C: Uncharacterized protein lp_1622
D: Uncharacterized protein lp_1622
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3808
Polymers101,9964
Non-polymers3844
Water13,349741
1
A: Uncharacterized protein lp_1622
B: Uncharacterized protein lp_1622
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1904
Polymers50,9982
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-19.1 kcal/mol
Surface area18010 Å2
MethodPISA
2
C: Uncharacterized protein lp_1622
D: Uncharacterized protein lp_1622
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1904
Polymers50,9982
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-20.7 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.784, 194.031, 52.093
Angle α, β, γ (deg.)90.00, 115.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS A DIMER ACCORDING TO AGGREGATION SCREENING.

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Components

#1: Protein
Uncharacterized protein lp_1622


Mass: 25498.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarumLactiplantibacillus plantarum
Strain: WCFS1 / NCIMB 8826 / Gene: lp_1622 / Plasmid: pET21-23c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q88WK7, UniProt: F9UNZ6*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% PEG 3350, 0.2M Ammonium sulfate, 0.1M Sodium acetate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97885, 0.97938, 0.96785
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978851
20.979381
30.967851
ReflectionResolution: 2.2→50 Å / Num. all: 88438 / Num. obs: 88438 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 19.3 / Num. unique all: 9348 / % possible all: 79.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→44.67 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 660059.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4261 4.9 %RANDOM
Rwork0.181 ---
obs0.181 86629 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7811 Å2 / ksol: 0.345493 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å24.53 Å2
2---2.14 Å20 Å2
3----1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 20 741 7249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.214 610 4.8 %
Rwork0.181 12187 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4so4.parso4.top

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