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- PDB-2y0o: The structure of a D-lyxose isomerase from the sigmaB regulon of ... -

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Basic information

Entry
Database: PDB / ID: 2y0o
TitleThe structure of a D-lyxose isomerase from the sigmaB regulon of Bacillus subtilis
ComponentsPROBABLE D-LYXOSE KETOL-ISOMERASE
KeywordsISOMERASE / CARBOHYDRATE METABOLISM / METAL-BINDING / SUGAR ISOMERASE / STRESS RESPONSE
Function / homology
Function and homology information


D-lyxose ketol-isomerase activity / D-lyxose ketol-isomerase / carbohydrate metabolic process / metal ion binding
Similarity search - Function
RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ARSENIC / Probable D-lyxose ketol-isomerase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.229 Å
AuthorsMarles-Wright, J. / Lewis, R.J.
CitationJournal: Proteins / Year: 2011
Title: The Structure of a D-Lyxose Isomerase from the Sigmab Regulon of Bacillus Subtilis
Authors: Marles-Wright, J. / Lewis, R.J.
History
DepositionDec 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE D-LYXOSE KETOL-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8205
Polymers20,4871
Non-polymers3324
Water4,828268
1
A: PROBABLE D-LYXOSE KETOL-ISOMERASE
hetero molecules

A: PROBABLE D-LYXOSE KETOL-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,64010
Polymers40,9752
Non-polymers6658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3540 Å2
ΔGint-132.8 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.716, 42.619, 65.881
Angle α, β, γ (deg.)90.00, 121.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

21A-2051-

HOH

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Components

#1: Protein PROBABLE D-LYXOSE KETOL-ISOMERASE


Mass: 20487.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ZINC AND ARSENIC COORDINATION IN ACTIVE SITE
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS (bacteria)
Strain: 168 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P96578, D-lyxose ketol-isomerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ARS / ARSENIC / Arsenic


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M SODIUM CACODYLATE PH 6.5 0.2 M NACL 2.0 M AMMONIUM SULFATE 1UL:1UL DROPS WITH PROTEIN IN WATER AT 11.5 MG/ML

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 24, 2010 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.23→35.45 Å / Num. obs: 51297 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.229→34.872 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 16.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1782 2586 5 %
Rwork0.1453 --
obs0.147 51279 99.32 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.657 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 18.91 Å2
Baniso -1Baniso -2Baniso -3
1-5.0148 Å20 Å20.5039 Å2
2---0.6054 Å20 Å2
3----4.4094 Å2
Refinement stepCycle: LAST / Resolution: 1.229→34.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 12 268 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141465
X-RAY DIFFRACTIONf_angle_d1.5591996
X-RAY DIFFRACTIONf_dihedral_angle_d14.225557
X-RAY DIFFRACTIONf_chiral_restr0.107207
X-RAY DIFFRACTIONf_plane_restr0.008263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2291-1.2730.31012270.27244763X-RAY DIFFRACTION98
1.273-1.3240.23642510.20324827X-RAY DIFFRACTION99
1.324-1.38430.20532690.16454832X-RAY DIFFRACTION99
1.3843-1.45720.20152660.14024809X-RAY DIFFRACTION99
1.4572-1.54850.14842800.11154820X-RAY DIFFRACTION99
1.5485-1.66810.16412360.10974900X-RAY DIFFRACTION100
1.6681-1.8360.16842520.11564875X-RAY DIFFRACTION100
1.836-2.10160.15032610.12614915X-RAY DIFFRACTION100
2.1016-2.64770.1822610.14234949X-RAY DIFFRACTION100
2.6477-34.88560.17762830.15575003X-RAY DIFFRACTION100

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