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- PDB-2i22: Crystal structure of Escherichia coli phosphoheptose isomerase in... -

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Basic information

Entry
Database: PDB / ID: 2i22
TitleCrystal structure of Escherichia coli phosphoheptose isomerase in complex with reaction substrate sedoheptulose 7-phosphate
ComponentsPhosphoheptose 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 / cytoplasm / cytosol
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
D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / Phosphoheptose isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBlakely, K. / Zhang, K. / DeLeon, G. / 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 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 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)92,3475
Polymers92,0574
Non-polymers2901
Water3,801211
1
A: Phosphoheptose isomerase
D: Phosphoheptose isomerase


Theoretical massNumber of molelcules
Total (without water)46,0282
Polymers46,0282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoheptose isomerase
C: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3183
Polymers46,0282
Non-polymers2901
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.045, 76.540, 78.316
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 192 / Label seq-ID: 21 - 212

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
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 / 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-I22 / D-ALTRO-HEPT-2-ULOSE 7-PHOSPHATE / 7-O-PHOSPHONO-D-ALTRO-HEPT-2-ULOSE / SEDOHEPTULOSE 7-PHOSPHATE


Mass: 290.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 3% PEG 8000, 0.002 M DTT, 3% 1,6-hexanediol, 0.01 M Hepes, 0.1 M 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: May 16, 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: 2.79→47.39 Å / Num. all: 20533 / Num. obs: 20533 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.79→2.89 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TK9

1tk9


Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.346 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25699 1478 7.3 %RANDOM
Rwork0.20297 ---
obs0.20694 18807 100 %-
all-18807 --
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: 44.337 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.51 Å2
2---0.34 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 0 18 211 5665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0225521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8451.9617423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00324.217249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.23415993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4831540
X-RAY DIFFRACTIONr_chiral_restr0.1870.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3010.23076
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.350.23871
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2373
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.211
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0391.53631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.85325572
X-RAY DIFFRACTIONr_scbond_it3.8332130
X-RAY DIFFRACTIONr_scangle_it5.4384.51851
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1357 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.40.5
2Bmedium positional0.430.5
3Cmedium positional0.440.5
4Dmedium positional0.370.5
1Amedium thermal2.362
2Bmedium thermal2.762
3Cmedium thermal2.622
4Dmedium thermal2.532
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 114 -
Rwork0.276 1364 -
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)
12.9855-0.42630.42081.2171-0.11981.19760.03270.1950.125-0.2877-0.0132-0.01320.1191-0.031-0.01960.090.015-0.0712-0.13990.1004-0.121519.18676.0661-6.9811
20.6706-0.18570.75741.8789-1.64682.5571-0.1308-0.07310.12470.18870.2099-0.36710.19020.1829-0.0790.00640.0358-0.1283-0.2640.0283-0.09839.3619-6.102421.3884
31.9924-0.01610.94621.2955-0.6291.3842-0.2365-0.436-0.01210.44840.07290.1496-0.026-0.02910.16370.1176-0.0114-0.0247-0.1361-0.0163-0.178520.4471-0.674135.8063
41.40710.0338-0.03441.7452-0.48652.8663-0.02650.15790.1034-0.16820.00630.42250.1528-0.55020.0202-0.05940-0.1758-0.15050.0327-0.014-0.28191.02285.5951
5183.5654-30.8749-58.88146.5851-20.675541.4775-0.2832-0.44-0.6-0.1643-0.18370.65450.4628-1.33080.46690.11820.005-0.2327-0.0141-0.06130.04528.5725-12.9927.1887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 192
2X-RAY DIFFRACTION2B1 - 192
3X-RAY DIFFRACTION3C1 - 192
4X-RAY DIFFRACTION4D1 - 192
5X-RAY DIFFRACTION5B900

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