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- PDB-3l6i: Crystal structure of the uncharacterized lipoprotein yceb from e.... -

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Basic information

Entry
Database: PDB / ID: 3l6i
TitleCrystal structure of the uncharacterized lipoprotein yceb from e. coli at the resolution 2.0a. northeast structural genomics consortium target er542
ComponentsUncharacterized lipoprotein yceB
Keywordsstructure genomics / unknown function / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Cell membrane / Lipoprotein / Membrane / Palmitate
Function / homologyUncharacterised protein PF07273 family, DUF1439 / Protein of unknown function DUF1439 / Protein of unknown function (DUF1439) / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Alpha Beta / Uncharacterized lipoprotein YceB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.011 Å
AuthorsKuzin, A.P. / Neely, H. / Seetharaman, J. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Neely, H. / Seetharaman, J. / Chen, C.X. / 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 the uncharacterized lipoprotein yceb from e. coli at the resolution 2.0a. northeast structural genomics consortium target er542
Authors: Kuzin, A.P. / Neely, H. / Seetharaman, J. / Chen, C.X. / 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
DepositionDec 23, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJan 26, 2010ID: 3EYR
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized lipoprotein yceB
B: Uncharacterized lipoprotein yceB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5274
Polymers41,4812
Non-polymers462
Water2,522140
1
A: Uncharacterized lipoprotein yceB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7642
Polymers20,7411
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized lipoprotein yceB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7642
Polymers20,7411
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uncharacterized lipoprotein yceB
hetero molecules

B: Uncharacterized lipoprotein yceB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5274
Polymers41,4812
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
Buried area1170 Å2
ΔGint-13 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.050, 174.550, 43.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1-

NA

21B-2-

NA

31A-253-

HOH

41B-232-

HOH

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Components

#1: Protein Uncharacterized lipoprotein yceB


Mass: 20740.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yceB, b1063, JW1050 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: P0AB26
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.3M NA MALONATE, 0.05M BIS TRIS, PROPANE PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 2008 / Details: mirror
RadiationMonochromator: MONOCHROMATIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.01→19.89 Å / Num. obs: 50815 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 39.6
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.011→19.793 Å / SU ML: 0.3 / σ(F): 1 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 1381 5.1 %
Rwork0.2051 --
obs0.2072 27060 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.168 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 2.011→19.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 2 140 2826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082742
X-RAY DIFFRACTIONf_angle_d1.2513706
X-RAY DIFFRACTIONf_dihedral_angle_d19.6681042
X-RAY DIFFRACTIONf_chiral_restr0.08425
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0113-2.08310.24291240.21632297X-RAY DIFFRACTION87
2.0831-2.16640.29191240.21152371X-RAY DIFFRACTION90
2.1664-2.26490.29121290.20962476X-RAY DIFFRACTION93
2.2649-2.38410.26851330.21312514X-RAY DIFFRACTION94
2.3841-2.53320.25391370.21652569X-RAY DIFFRACTION97
2.5332-2.72830.27481440.23812635X-RAY DIFFRACTION98
2.7283-3.00210.29661500.2232625X-RAY DIFFRACTION99
3.0021-3.43450.27421450.20442689X-RAY DIFFRACTION100
3.4345-4.31970.20731480.17072730X-RAY DIFFRACTION100
4.3197-19.79350.20991470.19782773X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 27.7927 Å / Origin y: 85.8457 Å / Origin z: 23.7622 Å
111213212223313233
T0.1417 Å2-0.0123 Å2-0.0011 Å2-0.1537 Å20.04 Å2--0.2406 Å2
L0.761 °2-1.4802 °2-0.0613 °2-1.7174 °20.226 °2---0.0177 °2
S0.067 Å °0.0497 Å °-0.0341 Å °-0.2115 Å °-0.029 Å °0.0414 Å °-0.0052 Å °0.0002 Å °-0.0026 Å °
Refinement TLS groupSelection details: all

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