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- PDB-1xiz: Structural Genomics, The crystal structure of domain IIA of putat... -

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Basic information

Entry
Database: PDB / ID: 1xiz
TitleStructural Genomics, The crystal structure of domain IIA of putative phosphotransferase system specific for mannitol/fructose from Salmonella typhimurium
Componentsputative phosphotransferase system mannitol/fructose-specific IIA domain
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / IIA domain / protein structure initiative / Midwest Center for Structural Genomics / MCSG / PSI
Function / homology
Function and homology information


: / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphotransferase system mannitol/fructose-specific IIA domain containing protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, R. / Joachimiak, G. / Otwinowski, Z. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of domain IIA of putative phosphotransferase system specific for mannitol/fructose from Salmonella typhimurium
Authors: Zhang, R. / Joachimiak, G. / Otwinowski, Z. / Collart, F. / Joachimiak, A.
History
DepositionSep 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative phosphotransferase system mannitol/fructose-specific IIA domain
B: putative phosphotransferase system mannitol/fructose-specific IIA domain


Theoretical massNumber of molelcules
Total (without water)36,0492
Polymers36,0492
Non-polymers00
Water2,954164
1
A: putative phosphotransferase system mannitol/fructose-specific IIA domain


Theoretical massNumber of molelcules
Total (without water)18,0241
Polymers18,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative phosphotransferase system mannitol/fructose-specific IIA domain


Theoretical massNumber of molelcules
Total (without water)18,0241
Polymers18,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.875, 48.138, 123.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein putative phosphotransferase system mannitol/fructose-specific IIA domain


Mass: 18024.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZL18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.1 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.9465
DetectorType: SBC-2 / Detector: CCD / Date: May 29, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.94651
ReflectionResolution: 2→50 Å / Num. all: 37329 / Num. obs: 37292 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.34
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.18 / Num. unique all: 3706 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→33.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 537142.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1796 5.1 %RANDOM
Rwork0.203 ---
all0.208 37329 --
obs0.203 35358 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0796 Å2 / ksol: 0.350699 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å20 Å2
2--0.77 Å20 Å2
3----4.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→33.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 0 164 2639
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 287 5.2 %
Rwork0.273 5224 -
obs--89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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