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- PDB-2i2w: Crystal Structure of Escherichia Coli Phosphoheptose Isomerase -

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Basic information

Entry
Database: PDB / ID: 2i2w
TitleCrystal Structure of Escherichia Coli Phosphoheptose Isomerase
ComponentsPhosphoheptose isomeraseD-sedoheptulose 7-phosphate isomerase
KeywordsISOMERASE / LIPOPOLYSACCHARIDE BIOSYNTHESIS / PHOSPHOHEPTOSE ISOMERASE
Function / homology
Function and homology information


D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / lipopolysaccharide core region biosynthetic process / carbohydrate derivative binding / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Phosphoheptose isomerase / GmhA/DiaA / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoheptose isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDeLeon, G. / Blakely, K. / Zhang, K. / Wright, G. / Junop, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure and Function of Sedoheptulose-7-phosphate Isomerase, a Critical Enzyme for Lipopolysaccharide Biosynthesis and a Target for Antibiotic Adjuvants
Authors: Taylor, P.L. / Blakely, K.M. / de Leon, G.P. / Walker, J.R. / McArthur, F. / Evdokimova, E. / Zhang, K. / Valvano, M.A. / Wright, G.D. / Junop, M.S.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS' ANALYTICAL ULTRACENTRIFUGATION AND GEL FILTRATION EXPERIMENTS SHOW THAT THE BIOLOGICAL ASSEMBLY IS A DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoheptose isomerase
B: Phosphoheptose isomerase
C: Phosphoheptose isomerase
D: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1495
Polymers92,0574
Non-polymers921
Water11,133618
1
A: Phosphoheptose isomerase
D: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1203
Polymers46,0282
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-27 kcal/mol
Surface area15850 Å2
MethodPISA, PQS
2
B: Phosphoheptose isomerase
C: Phosphoheptose isomerase


Theoretical massNumber of molelcules
Total (without water)46,0282
Polymers46,0282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-26 kcal/mol
Surface area15690 Å2
MethodPISA, PQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-62 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.930, 89.610, 106.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer generated from either the A and D or B and C monomers within the asymmetric unit.

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Components

#1: Protein
Phosphoheptose isomerase / D-sedoheptulose 7-phosphate isomerase / Sedoheptulose 7-phosphate isomerase


Mass: 23014.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gmhA, lpcA, tfrA, b0222 / Plasmid: pDEST17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P63224, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 3% PEG 8000, 0.002M DTT, 3% 1,6-hexanediol, 0.01M Hepes, 0.1M imidazole, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 22, 2005
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→45.9 Å / Num. all: 59294 / Num. obs: 59294 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.27 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.18 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→45.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.556 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21921 2996 5.1 %RANDOM
Rwork0.16994 ---
obs0.1723 56213 100 %-
all-56213 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 6 618 6254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.0225712
X-RAY DIFFRACTIONr_angle_refined_deg2.7731.9557683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9665733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99224.231260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.067151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5151540
X-RAY DIFFRACTIONr_chiral_restr0.2490.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.024280
X-RAY DIFFRACTIONr_nbd_refined0.2390.22993
X-RAY DIFFRACTIONr_nbtor_refined0.3260.24064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2484
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.218
X-RAY DIFFRACTIONr_mcbond_it2.1951.53633
X-RAY DIFFRACTIONr_mcangle_it3.40925780
X-RAY DIFFRACTIONr_scbond_it4.99232079
X-RAY DIFFRACTIONr_scangle_it7.8094.51903
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 222 -
Rwork0.289 4113 -
obs--100 %
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)
10.6738-0.0759-0.32570.04830.06790.18190.07580.09840.1477-0.0207-0.0319-0.0577-0.007-0.0124-0.0439-0.03670.0105-0.0095-0.060.01990.00760.659481.2834.8142
30.0194-0.06910.05070.55080.14220.47340.04160.06110.0115-0.1133-0.0269-0.00570.08440.0447-0.0148-0.00740.0008-0.0176-0.0285-0.031-0.070664.020946.638626.3135
50.2062-0.2566-0.11870.32850.09020.4299-0.02990.0091-0.02530.00610.00850.08750.08870.02360.0215-0.02850.00230.0045-0.05050.0136-0.021757.603942.398649.1417
70.6444-0.1368-0.2610.3493-0.05760.14560.03330.01760.07220.06160.0530.02330.04680.006-0.0864-0.0394-0.0058-0.0123-0.0440.0126-0.03244.272875.588251.5627
910.6596-1.1708-6.258812.43414.691322.017-0.0117-0.0234-0.18910.1749-0.02730.02790.31090.0150.0390.00220.00040.00030.0009-0.00090.001429.767865.981960.9555
100.2931-0.19650.02110.2339-0.03520.1533-0.009-0.010.0186-0.01320.00240.030.02460.00950.0066-0.0494-0.0141-0.0149-0.02470.0082-0.029457.300862.634641.5134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 19221 - 212
3X-RAY DIFFRACTION3BB1 - 19221 - 212
5X-RAY DIFFRACTION5CC1 - 19221 - 212
7X-RAY DIFFRACTION7DD1 - 19221 - 212
9X-RAY DIFFRACTION9DE1961
10X-RAY DIFFRACTION10A - DF - I193 - 3551 - 159

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