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- PDB-4q6j: Crystal Structure of EAL domain Protein from Listeria monocytogen... -

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Basic information

Entry
Database: PDB / ID: 4q6j
TitleCrystal Structure of EAL domain Protein from Listeria monocytogenes EGD-e
ComponentsLmo0131 protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TIM barrel / alpha-betafold
Function / homology
Function and homology information


EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / PHOSPHATE ION / Lmo0131 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.369 Å
AuthorsKim, Y. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of EAL domain Protein from Listeria monocytogenes EGD-e
Authors: Kim, Y. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0131 protein
B: Lmo0131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,79019
Polymers58,6412
Non-polymers1,14917
Water7,080393
1
A: Lmo0131 protein
B: Lmo0131 protein
hetero molecules

A: Lmo0131 protein
B: Lmo0131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,58138
Polymers117,2834
Non-polymers2,29834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16100 Å2
ΔGint30 kcal/mol
Surface area39890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.771, 72.483, 77.573
Angle α, β, γ (deg.)90.00, 125.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lmo0131 protein


Mass: 29320.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0131 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q8YAJ4

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Non-polymers , 5 types, 410 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.8 M sodium phosphate, 0.8 M postassium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
Reflection twinOperator: -h-2*l,-k,l / Fraction: 0.5
ReflectionResolution: 1.37→50 Å / Num. all: 120312 / Num. obs: 120312 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 17.02 Å2 / Rsym value: 0.083 / Net I/σ(I): 13.1
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4456 / Rsym value: 0.6 / % possible all: 72.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1621)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.369→30.069 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.92 / Stereochemistry target values: TWIN_LSQ_F
Details: both Freidel pair reflections were used in refinement, which is reflected the refinement statistics
RfactorNum. reflection% reflectionSelection details
Rfree0.169 6111 5.08 %random
Rwork0.137 ---
all0.14 120309 --
obs0.14 120309 96.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.369→30.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 72 393 4448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134390
X-RAY DIFFRACTIONf_angle_d1.4155927
X-RAY DIFFRACTIONf_dihedral_angle_d15.0031694
X-RAY DIFFRACTIONf_chiral_restr0.089660
X-RAY DIFFRACTIONf_plane_restr0.006762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.3698-1.39340.30852060.25764176438268
1.3934-1.41880.27512740.24775001527580
1.4188-1.44610.25512820.23495598588090
1.4461-1.47560.2313360.21085671600791
1.4756-1.50770.23393050.19475746605192
1.5077-1.54270.21762830.19615819610293
1.5427-1.58130.22132970.19235771606893
1.5813-1.6240.22332900.18975774606493
1.624-1.67180.21613020.18485830613293
1.6718-1.72580.20482950.18625819611493
1.7258-1.78740.20763140.18085832614694
1.7874-1.8590.20113390.1765839617893
1.859-1.94350.18533110.1695835614694
1.9435-2.0460.19393070.16595906621394
2.046-2.17410.17922810.15275893617495
2.1741-2.34180.18123160.14335904622094
2.3418-2.57720.15423440.12545899624394
2.5772-2.94960.1663160.11385949626595
2.9496-3.7140.12363030.09346009631295
3.714-24.23430.12273200.09216001632194

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