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- PDB-1x92: CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA PHOSPHOHEPTOSE ISOMER... -

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Basic information

Entry
Database: PDB / ID: 1x92
TitleCRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA PHOSPHOHEPTOSE ISOMERASE IN COMPLEX WITH REACTION PRODUCT D-GLYCERO-D-MANNOPYRANOSE-7-PHOSPHATE
ComponentsPHOSPHOHEPTOSE ISOMERASE
KeywordsISOMERASE / MIDWEST CENTRE FOR STRUCTURAL GENOMICS / SIS Domain / a/b protein / lipopolysaccharide biosynthesis / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DnaA-DiaA complex / 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 / positive regulation of DNA-templated DNA replication initiation / zinc ion binding / 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
Chem-M7P / Phosphoheptose isomerase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWalker, J.R. / Evdokimova, E. / Kudritska, M. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
Citation
Journal: 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.
#1: Journal: Microbiology / Year: 2002
Title: Novel pathways for biosynthesis of nucleotide-activated glycero-manno-heptose precursors of bacterial glycoproteins and cell surface polysaccharides
Authors: Valvano, M.A. / Messner, P. / Kosma, P.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Biosynthesis of inner core lipopolysaccharide in enteric bacteria identification and characterization of a conserved phosphoheptose isomerase
Authors: Brooke, J.S. / Valvano, M.A.
History
DepositionAug 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8374
Polymers43,2572
Non-polymers5802
Water3,531196
1
A: PHOSPHOHEPTOSE ISOMERASE
B: PHOSPHOHEPTOSE ISOMERASE
hetero molecules

A: PHOSPHOHEPTOSE ISOMERASE
B: PHOSPHOHEPTOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6758
Polymers86,5144
Non-polymers1,1614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area17400 Å2
ΔGint-48 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.338, 126.338, 113.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the assembly can be generated by apply the matrix: 0.5000 0.8660 0.0000 0.8660 -.5000 0.0000 0.0000 0.0000 -1.000 63.1685 -109.4127 -18.8724

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Components

#1: Protein PHOSPHOHEPTOSE ISOMERASE / APC5045


Mass: 21628.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lpcA, gmhA / Plasmid: modified pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q9HVZ0
#2: Sugar ChemComp-M7P / 7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose / D-GLYCERO-D-MANNOPYRANOSE-7-PHOSPHATE / 7-O-phosphono-D-glycero-alpha-D-manno-heptose / 7-O-phosphono-D-glycero-D-manno-heptose / 7-O-phosphono-D-glycero-manno-heptose


Type: D-saccharide, alpha linking / Mass: 290.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: D-SEDOHEPTULOSE-7-PHOSPHATE, AMMONIUM SULPHATE, K/NA TARTRATE, NA CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.07229 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 6, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111)DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07229 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 24669 / Num. obs: 24669 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 25.03
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 6.17 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE DETERMINED BY MAD PHASING IN SPACEGROUP P21212

Resolution: 2.3→39.34 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2787370.22 / 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
Rfree0.221 1222 5 %RANDOM
Rwork0.176 ---
obs0.176 24221 99.9 %-
all-24221 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.4621 Å2 / ksol: 0.353441 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.75 Å21.56 Å20 Å2
2---4.75 Å20 Å2
3---9.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 36 196 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it4.082.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 190 4.8 %
Rwork0.192 3752 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SP7F_2_PRO.PARAMSP7F_2_PRO.TOP

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