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- PDB-3kmh: Crystal Structure of a Novel Sugar Isomerase from E. coli O157:H7 -

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Basic information

Entry
Database: PDB / ID: 3kmh
TitleCrystal Structure of a Novel Sugar Isomerase from E. coli O157:H7
ComponentsD-lyxose isomerase
KeywordsISOMERASE / cupin beta-barrel / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


isomerase activity / metal ion binding
Similarity search - Function
D-lyxose isomerase / : / D-lyxose isomerase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / PHENOL / : / D-lyxose/D-mannose family sugar isomerase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
Authorsvan Staalduinen, L.M. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7.
Authors: van Staalduinen, L.M. / Park, C.S. / Yeom, S.J. / Adams-Cioaba, M.A. / Oh, D.K. / Jia, Z.
History
DepositionNov 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-lyxose isomerase
B: D-lyxose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6408
Polymers56,1932
Non-polymers4476
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-20 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.350, 75.315, 61.778
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-lyxose isomerase


Mass: 28096.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: Escherichia coli O157:H7 EDL933 / Gene: ECs5070, Z5688 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 (DE3) / References: UniProt: Q8X5Q7, D-lyxose ketol-isomerase

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Non-polymers , 5 types, 496 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.65
Details: 10.5% PEG 550 MME, 10 mM Phenol, 0.1 M sodium acetate, pH 4.65, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.97561 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 26, 2007
RadiationMonochromator: Double crystal monochromator with fixed exit geometry; Bragg angle range is 7.55 degrees - 28 degrees; sagitally focusing Si(111) crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97561 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. all: 62650 / Num. obs: 62650 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rsym value: 0.061 / Net I/σ(I): 32.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 5.7 / Rsym value: 0.329 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL2Mapmodel building
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→29.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.585 / SU ML: 0.057 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21252 3175 5.1 %RANDOM
Rwork0.19139 ---
obs0.19246 59447 96.86 %-
all-62650 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.033 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.58→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 25 490 4026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213628
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.9234926
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69224.456193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17415559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1781520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212859
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_it0.4871.52196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97723521
X-RAY DIFFRACTIONr_scbond_it1.64431432
X-RAY DIFFRACTIONr_scangle_it2.5834.51405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.576→1.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 191 -
Rwork0.237 3453 -
obs--76.68 %

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