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- PDB-1g98: CRYSTAL STRUCTURE ANALYSIS OF RABBIT PHOSPHOGLUCOSE ISOMERASE COM... -

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Basic information

Entry
Database: PDB / ID: 1g98
TitleCRYSTAL STRUCTURE ANALYSIS OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH 5-PHOSPHOARABINONATE, A TRANSITION STATE ANALOGUE
ComponentsPHOSPHOGLUCOSE ISOMERASE
KeywordsISOMERASE / Phosphoglucose Isomerase / 5-phosphoarabinonate / transition state analogue
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 / gluconeogenesis / glycolytic process / 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
5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJeffery, C.J. / Hardre, R. / Salmon, L.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonate identifies the role of Glu357 in catalysis.
Authors: Jeffery, C.J. / Hardre, R. / Salmon, L.
History
DepositionNov 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2001Provider: 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 ...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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOGLUCOSE ISOMERASE
B: PHOSPHOGLUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1474
Polymers125,6552
Non-polymers4922
Water16,069892
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-79 kcal/mol
Surface area36280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.829, 116.554, 271.824
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-992-

HOH

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Components

#1: Protein PHOSPHOGLUCOSE ISOMERASE / E.C.5.3.1.9


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: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution: 15-20mg/ml PGI, 10mM imidazole (pH 7.5), 50mM KCl, 3mMNaN3, 5mM 5PAH reservoir solution: 10-15% PEG 8000, 250mM magnesium acetate, 100mM sodium cacodylate (pH6.5). VAPOR ...Details: protein solution: 15-20mg/ml PGI, 10mM imidazole (pH 7.5), 50mM KCl, 3mMNaN3, 5mM 5PAH reservoir solution: 10-15% PEG 8000, 250mM magnesium acetate, 100mM sodium cacodylate (pH6.5). VAPOR DIFFUSION, HANGING DROP at 298K, pH 7.0, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
210 mMimidazole1drop
350 mM1dropKCl
43 mM1dropNaN3
55 mM5PAH1drop
610-15 %PEG80001reservoir
7250 mMmagnesium acetate1reservoir
8100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→8 Å / Num. all: 95997 / Num. obs: 95997 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 22.646 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 26.86
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.88 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 15.45 / Num. unique all: 10080 / Rsym value: 0.082 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 486988
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

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

1dqr


Resolution: 1.9→8 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 9635 10 %random
Rwork0.211 ---
all-95997 --
obs-95997 93.6 %-
Displacement parametersBiso mean: 25.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8790 0 30 892 9712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d22.76
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.274 969 -
Rwork0.226 --
obs-8963 98 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.76
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.274 / Rfactor Rwork: 0.226 / Rfactor obs: 0.226

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