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- PDB-3trj: Structure of a phosphoheptose isomerase from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 3trj
TitleStructure of a phosphoheptose isomerase from Francisella tularensis
ComponentsPhosphoheptose isomeraseD-sedoheptulose 7-phosphate isomerase
KeywordsISOMERASE / Lipopolysaccharide biosynthesis
Function / homology
Function and homology information


Isomerases / carbohydrate derivative metabolic process / carbohydrate derivative binding / isomerase activity
Similarity search - Function
GmhA/DiaA / SIS domain / SIS domain / SIS domain profile. / 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 speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Plos One / Year: 2013
Title: Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.
Authors: Chaudhury, S. / Abdulhameed, M.D. / Singh, N. / Tawa, G.J. / D'haeseleer, P.M. / Zemla, A.T. / Navid, A. / Zhou, C.E. / Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Love, J. / Graf, J.F. / ...Authors: Chaudhury, S. / Abdulhameed, M.D. / Singh, N. / Tawa, G.J. / D'haeseleer, P.M. / Zemla, A.T. / Navid, A. / Zhou, C.E. / Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Love, J. / Graf, J.F. / Rozak, D.A. / Dankmeyer, J.L. / Amemiya, K. / Daefler, S. / Wallqvist, A.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references / Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,3184
Polymers86,3184
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-118 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.131, 98.131, 149.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 21579.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_1681c, lpcA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NEF5, Isomerases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 M magnesium chloride, 30% PEG400, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 14, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 20691 / Num. obs: 20671 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.759.10.5721100
2.75-2.890.5381100
2.8-2.859.20.4581100
2.85-2.919.10.4131100
2.91-2.979.10.391100
2.97-3.049.20.3481100
3.04-3.129.10.2831100
3.12-3.29.10.251100
3.2-3.299.20.2231100
3.29-3.49.20.1961100
3.4-3.529.20.1861100
3.52-3.669.30.151100
3.66-3.839.40.131100
3.83-4.039.50.1261100
4.03-4.289.60.1031100
4.28-4.619.80.0931100
4.61-5.0710.10.0891100
5.07-5.810.20.0941100
5.8-7.310.20.0751100
7.3-309.20.048197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TK9

1tk9


Resolution: 2.8→24.166 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 0 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2778 944 5.14 %
Rwork0.2262 --
obs0.2288 18364 98.73 %
all-19556 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.001 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.1953 Å20 Å2-0 Å2
2--12.1953 Å2-0 Å2
3----19.1458 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5489 0 0 19 5508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025557
X-RAY DIFFRACTIONf_angle_d0.5827539
X-RAY DIFFRACTIONf_dihedral_angle_d11.5241985
X-RAY DIFFRACTIONf_chiral_restr0.04919
X-RAY DIFFRACTIONf_plane_restr0.001983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94740.39471380.31142446X-RAY DIFFRACTION100
2.9474-3.13170.37241400.30822433X-RAY DIFFRACTION99
3.1317-3.37290.37741450.28362467X-RAY DIFFRACTION100
3.3729-3.71130.28521390.24652433X-RAY DIFFRACTION98
3.7113-4.24580.25041160.20812452X-RAY DIFFRACTION97
4.2458-5.33970.21881330.18072516X-RAY DIFFRACTION98
5.3397-24.16650.22791330.19672673X-RAY DIFFRACTION99

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