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- PDB-3gx1: Crystal structure of a domain of lin1832 from Listeria innocua -

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Basic information

Entry
Database: PDB / ID: 3gx1
TitleCrystal structure of a domain of lin1832 from Listeria innocua
ComponentsLin1832 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC63308.2 / lin1832 / Listeria innocua / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / transcription factor binding / kinase activity / membrane => GO:0016020 / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. ...PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Winged helix DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria innocua Clip11262 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsTan, K. / Rakowski, E. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain of lin1832 from Listeria innocua
Authors: Tan, K. / Rakowski, E. / Cobb, G. / Joachimiak, A.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin1832 protein
B: Lin1832 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,32212
Polymers29,3622
Non-polymers96110
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-20.2 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.852, 152.852, 45.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN. IT IS PREDICTED THAT CHAINS A AND B FORM A DIMER.

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Components

#1: Protein Lin1832 protein


Mass: 14680.861 Da / Num. of mol.: 2 / Fragment: Domain: UNP residues 542-668
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua Clip11262 (bacteria) / Strain: Clip11262 / Serovar 6a / Gene: lin1832 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q92AT7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 4.5 Å3/Da / Density % sol: 72.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M MgSO4, 0.1M MES, pH 6.5, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2009 / Details: Mirror
RadiationMonochromator: Si(111) crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→42 Å / Num. all: 23117 / Num. obs: 23117 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 45.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 3.8 / % possible all: 71.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 13.289 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24088 1180 5.1 %RANDOM
Rwork0.2116 ---
all0.21307 21879 --
obs0.21307 21879 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 50 22 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221977
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9282.0222672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10325.9767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.04115392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.646158
X-RAY DIFFRACTIONr_chiral_restr0.1450.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211336
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7521.51248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40322034
X-RAY DIFFRACTIONr_scbond_it3.0623729
X-RAY DIFFRACTIONr_scangle_it4.724.5638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 68 -
Rwork0.305 1206 -
obs-1274 71.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.19743.1141-1.07746.1032-1.96081.59380.101-0.4387-0.47750.3441-0.15230.38810.0667-0.02290.05130.293-0.04240.03780.27330.08390.263344.667-2210.253
26.20121.378-1.1656.3146-1.48441.33380.2058-0.19530.12360.23260.06080.6685-0.04140.0818-0.26660.2628-0.01680.01160.30980.02260.087256.165-2.0091.598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A539 - 664
2X-RAY DIFFRACTION2B540 - 665

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