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- PDB-1hm5: CRYSTAL STRUCTURE ANALYSIS OF THE RABBIT D-GLUCOSE 6-PHOSPHATE IS... -

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Basic information

Entry
Database: PDB / ID: 1hm5
TitleCRYSTAL STRUCTURE ANALYSIS OF THE RABBIT D-GLUCOSE 6-PHOSPHATE ISOMERASE (NO LIGAND BOUND)
ComponentsPHOSPHOGLUCOSE ISOMERASE
KeywordsISOMERASE / dimer
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / cytokine activity / glycolytic process / gluconeogenesis / extracellular space / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArsenieva, D.A. / Jeffery, C.J. / Hardre, R. / Salmon, L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Conformational Changes in Phosphoglucose Isomerase Induced by Ligand Binding
Authors: Arsenieva, D.A. / Jeffery, C.J.
History
DepositionDec 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOGLUCOSE ISOMERASE
B: PHOSPHOGLUCOSE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)125,6552
Polymers125,6552
Non-polymers00
Water16,682926
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-70 kcal/mol
Surface area37010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.756, 115.966, 271.845
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-971-

HOH

21B-853-

HOH

DetailsThe active enzyme is a dimer. A complete dimer is in the asymmetric unit.

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Components

#1: Protein PHOSPHOGLUCOSE ISOMERASE / E.C.5.3.1.9 / D-GLUCOSE 6-PHOSPHATE ISOMERASE


Mass: 62827.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RABBIT SKELETAL MUSCLE TISSUE / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q9N1E2, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 14% PEG 8000, 0.1M sodium cacodylate, 0.25M magnesium chloride, pH 6.6 mixed 1:1 with protein in solution 10mM imidazole, 50mM potassium chloride, pH7.5, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
250 mM1dropKCl
310 mMimidazole1droppH7.5
412-14 %(w/v)PEG80001reservoir
5250 mMmagnesium acetate1reservoir
6100 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2000 / Details: mirrors
RadiationMonochromator: bent conical Si-mirror (Rh coating) bend cylindrical Ge(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 105425 / Num. obs: 105425 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 25.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.72 / Num. unique all: 5684 / % possible all: 47.5
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 398627 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 47.5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DQR

1dqr


Resolution: 1.8→10 Å / Isotropic thermal model: none / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 10314 10 %RANDOM
Rwork0.1832 ---
all0.186 120144 --
obs0.183 102691 85.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8816 0 0 926 9742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.276
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.007
X-RAY DIFFRACTIONc_improper_angle_d0.928
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.277 532 -
Rwork0.252 --
obs-5011 48 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.186 / Rfactor obs: 0.183 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.007
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.928
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / Rfactor Rwork: 0.252

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