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- PDB-2p0y: Crystal structure of Q88YI3_LACPL from Lactobacillus plantarum. N... -

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Basic information

Entry
Database: PDB / ID: 2p0y
TitleCrystal structure of Q88YI3_LACPL from Lactobacillus plantarum. Northeast Structural Genomics Consortium target LpR6
ComponentsHypothetical protein lp_0780Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / LpR6 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


regulation of cell shape / cytoplasm
Similarity search - Function
Gluconeogenesis factor / CofD-like domains / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative gluconeogenesis factor / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsBenach, J. / Chen, Y. / Seetharaman, J. / Chi, K.H. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Benach, J. / Chen, Y. / Seetharaman, J. / Chi, K.H. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Q88YI3_LACPL from Lactobacillus plantarum.
Authors: Benach, J. / Chen, Y. / Seetharaman, J. / Chi, K.H. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein lp_0780


Theoretical massNumber of molelcules
Total (without water)38,1381
Polymers38,1381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.658, 78.130, 149.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hypothetical protein lp_0780 / Hypothesis


Mass: 38137.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: NCIMB 8826, WCFS1 / Gene: lp_0780 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q88YI3, UniProt: F9UM03*PLUS

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 278 K / Method: microbatch under oil
Details: 2.0 M Sodium chloride, 10 % PEG 6000, MICROBATCH UNDER OIL, temperature 278K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97921, 0.97950, 0.96791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.97951
30.967911
Reflection

D res high: 3 Å / D res low: 50 Å / Redundancy: 3.8 %

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
112.81241570.0861.243264398.7
211.21244880.11.313265099.3
39.21219620.1311.363227999.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.46509910.0261.1223.8
5.136.4699.910.061.0443.8
4.485.1310010.0621.173.9
4.074.4899.910.0761.1993.9
3.784.0799.910.0961.2363.8
3.563.7810010.1251.2153.8
3.383.5610010.1651.3053.8
3.233.3810010.2021.3163.8
3.113.2310010.2731.43.8
33.1188.710.3641.43.6
6.465099.120.0261.153.8
5.136.4699.920.0681.1133.8
4.485.1310020.071.2453.9
4.074.4810020.0871.2773.9
3.784.0799.920.1171.4113.8
3.563.7810020.1551.3633.8
3.383.5610020.2081.423.8
3.233.3810020.2611.3873.8
3.113.2310020.3491.4223.8
33.1194.320.471.3593.6
6.465099.230.0291.0783.8
5.136.4610030.091.2343.8
4.485.1310030.0891.2763.9
4.074.4810030.1181.3933.8
3.784.0799.930.1661.3853.8
3.563.7810030.2211.4033.8
3.383.5699.930.3061.4473.8
3.233.3810030.3771.443.8
3.113.2310030.4931.493.7
33.1199.730.631.4443.6
ReflectionResolution: 3→50 Å / Num. obs: 15950 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.114 / Χ2: 1.66 / Net I/σ(I): 9.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.397 / Num. unique all: 1603 / Χ2: 1.085 / % possible all: 96.6

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Phasing

Phasing dmFOM : 0.67 / FOM acentric: 0.68 / FOM centric: 0.63 / Reflection: 7613 / Reflection acentric: 6637 / Reflection centric: 976
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.4-31.9410.920.960.84379259120
5.3-8.40.790.820.641102909193
4.2-5.30.810.820.7313781185193
3.7-4.20.770.780.6813201176144
3.2-3.70.590.60.5222462021225
3-3.20.370.370.311881087101

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / FOM work R set: 0.736 / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.339 1281 8 %
Rwork0.274 --
obs-13650 85.4 %
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 25.126 Å2
Baniso -1Baniso -2Baniso -3
1-2.701 Å20 Å20 Å2
2---4.728 Å20 Å2
3---2.028 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 0 0 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.9591.5
X-RAY DIFFRACTIONc_scbond_it3.2192
X-RAY DIFFRACTIONc_mcangle_it3.1732
X-RAY DIFFRACTIONc_scangle_it5.0712.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
3-3.040.519480.346413461
3.04-3.080.352440.309398442
3.08-3.130.333460.313409455
3.13-3.180.34510.332414465
3.18-3.230.3320.268483515
3.23-3.290.354390.259481520
3.29-3.350.342440.301454498
3.35-3.410.324580.289440498
3.41-3.480.444470.303516563
3.48-3.550.314390.287502541
3.55-3.640.425510.265443494
3.64-3.730.364550.287557612
3.73-3.830.299690.251468537
3.83-3.940.31490.209542591
3.94-4.060.312660.245512578
4.06-4.210.255450.239507552
4.21-4.380.233580.215579637
4.38-4.570.219420.203519561
4.57-4.810.268570.231552609
4.81-5.110.332500.237530580
5.11-5.490.494480.314548596
5.49-6.030.38650.305526591
6.03-6.870.323640.287505569
6.87-8.550.355590.304538597
8.55-200.415550.351533588
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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