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- PDB-3oou: The structure of a protein with unkown function from Listeria innocua -

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Basic information

Entry
Database: PDB / ID: 3oou
TitleThe structure of a protein with unkown function from Listeria innocua
ComponentsLin2118 protein
Keywordsstructural genomics / unknown function / Protein Structure Initiative / PSI-2 / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeodomain-like ...Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsFan, Y. / Mack, J. / Feldman, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a protein with unkown function from Listeria innocua
Authors: Fan, Y. / Mack, J. / Feldman, B. / Joachimiak, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin2118 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1923
Polymers12,9211
Non-polymers2712
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.891, 51.891, 75.384
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Lin2118 protein


Mass: 12921.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2118 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92A04
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 45.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M ammonium sulfate, 0.1M bis-tris pH5.5, 25%w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. all: 16695 / Num. obs: 16695 / % possible obs: 98.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 43.4
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.89 / Num. unique all: 780 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SBC-Collectcollectdata collection
SHELXDphasing
MLPHAREphasing
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.57→44.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.638 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21702 842 5 %RANDOM
Rwork0.19174 ---
all0.19297 15848 --
obs0.19297 15848 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.386 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.57→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 18 126 1022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022962
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9561303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2795118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15723.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05215175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.393156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02742
X-RAY DIFFRACTIONr_mcbond_it0.6841.5544
X-RAY DIFFRACTIONr_mcangle_it1.3082888
X-RAY DIFFRACTIONr_scbond_it23418
X-RAY DIFFRACTIONr_scangle_it3.2654.5408
X-RAY DIFFRACTIONr_rigid_bond_restr0.8553962
LS refinement shellResolution: 1.571→1.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 50 -
Rwork0.295 1166 -
obs--99.02 %
Refinement TLS params.Method: refined / Origin x: -0.1034 Å / Origin y: 34.1473 Å / Origin z: 17.611 Å
111213212223313233
T0.0259 Å2-0.0017 Å20.0048 Å2-0.0216 Å2-0.003 Å2--0.0121 Å2
L0.1434 °20.2269 °2-0.1732 °2-0.8658 °2-0.0878 °2--0.3731 °2
S-0.0402 Å °0.0222 Å °-0.0107 Å °-0.0152 Å °0.0391 Å °-0.0203 Å °0.0255 Å °-0.0399 Å °0.0011 Å °

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