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- PDB-1j3r: Crystal structure of Thermococcus litoralis phosphogrucose isomer... -

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Basic information

Entry
Database: PDB / ID: 1j3r
TitleCrystal structure of Thermococcus litoralis phosphogrucose isomerase complexed with gluconate-6-phosphate
ComponentsPhosphoglucose Isomerase
KeywordsISOMERASE / phosphoglucose isomerase / cupin superfamily / iron ion / archaea / gluconate 6-phosphate
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / iron ion binding / cytoplasm
Similarity search - Function
Glucose-6-phosphate isomerase, prokaryote / Glucose-6-phosphate isomerase, archaea/bacteria / Glucose-6-phosphate isomerase (GPI) / : / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
6-PHOSPHOGLUCONIC ACID / : / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.18 Å
AuthorsJeong, J.-J. / Fushinobu, S. / Ito, S. / Hidaka, M. / Shoun, H. / Wakagi, T.
Citation
Journal: To be Published
Title: Crystal structure of a novel cupin-type phosphoglucose isomerase
Authors: Jeong, J.-J. / Fushinobu, S. / Ito, S. / Hidaka, M. / Shoun, H. / Wakagi, T.
#1: Journal: FEBS Lett. / Year: 2003
Title: Characterization of the cupin-type phosphoglucose isomerase from the hyperthermophilic archaeon Thermococcus litoralis(1).
Authors: Jeong, J.-J. / Fushinobu, S. / Ito, S. / Jeon, B.-S. / Shoun, H. / Wakagi, T.
History
DepositionFeb 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglucose Isomerase
B: Phosphoglucose Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1085
Polymers43,5002
Non-polymers6083
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-58 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.670, 80.230, 130.040
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 in the asymmetric unit.

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Components

#1: Protein Phosphoglucose Isomerase


Mass: 21749.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (archaea) / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P84140, glucose-6-phosphate isomerase
#2: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.31 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG 8000, potassium phosphate, gluconate 6-phosphate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 30, 2002 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→40.12 Å / Num. all: 22995 / Num. obs: 22995 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.8
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 7.06 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J3P

1j3p


Resolution: 2.18→40.11 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1458307.62 / 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
Rfree0.263 1117 5 %RANDOM
Rwork0.218 ---
all0.22 23012 --
obs0.218 22345 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.3442 Å2 / ksol: 0.449829 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2---3.63 Å20 Å2
3---2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.18→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 35 273 3293
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 174 4.7 %
Rwork0.236 3535 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION36PG.PARAM6PG.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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