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- PDB-1qxr: Crystal structure of phosphoglucose isomerase from Pyrococcus fur... -

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Basic information

Entry
Database: PDB / ID: 1qxr
TitleCrystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with 5-phosphoarabinonate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / phosphoglucose isomerase / cupin fold / Pyrococcus furiosus / hyperthermophile / extremophile / aldose-ketose isomerase
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
NICKEL (II) ION / 5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / REFINEMENT / Resolution: 1.7 Å
AuthorsSwan, M.K. / Solomons, J.T.G. / Beeson, C.C. / Hansen, P. / Schonheit, P. / Davies, C.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structural evidence for a hydride transfer mechanism of catalysis in phosphoglucose isomerase from Pyrococcus furiosus
Authors: Swan, M.K. / Solomons, J.T.G. / Beeson, C.C. / Hansen, P. / Schonheit, P. / Davies, C.
#1: Journal: Protein Pept.Lett. / Year: 2003
Title: Crystallization and preliminary X-ray diffraction analysis of phosphoglucose isomerase from Pyrococcus furiosus
Authors: Swan, M.K. / Hansen, P. / Schonheit, P. / Davies, C.
History
DepositionSep 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The carboxylate oxygens of 5-phosphoarabinonate are labeled O1 and O1A in the pdb file ...HETEROGEN The carboxylate oxygens of 5-phosphoarabinonate are labeled O1 and O1A in the pdb file whereas in the published paper describing this structure these atoms are referred to as O1A and O1B, respectively.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6206
Polymers43,0112
Non-polymers6104
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-64 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.0, 39.7, 74.7
Angle α, β, γ (deg.)73.7, 78.5, 72.6
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glucose-6-phosphate isomerase / / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 21505.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PGIA OR PF0196 / Plasmid: pet17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P83194, glucose-6-phosphate isomerase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharideCarbohydrate / Mass: 246.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %(w/v)PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 Msodium acetate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 4, 2003 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→36.8 Å / Num. obs: 38279 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3618 / % possible all: 88.2
Reflection
*PLUS
Num. obs: 38270 / Num. measured all: 103907
Reflection shell
*PLUS
% possible obs: 88.2 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: REFINEMENT
Starting model: 1QXJ

1qxj


Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.52 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1940 5.1 %RANDOM
Rwork0.221 ---
all0.223 ---
obs0.223 38161 92.3 %-
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: 29.621 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å2-0.72 Å2-0.46 Å2
2---0.23 Å21.61 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 32 126 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223116
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9584220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7283372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.89415555
X-RAY DIFFRACTIONr_chiral_restr0.1070.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022390
X-RAY DIFFRACTIONr_nbd_refined0.2180.31309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.5299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.317
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.510
X-RAY DIFFRACTIONr_mcbond_it0.841.51852
X-RAY DIFFRACTIONr_mcangle_it1.48722988
X-RAY DIFFRACTIONr_scbond_it2.2731264
X-RAY DIFFRACTIONr_scangle_it3.6174.51232
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 142
Rwork0.372 2447
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.54

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