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- PDB-1dqr: CRYSTAL STRUCTURE OF RABBIT PHOSPHOGLUCOSE ISOMERASE, A GLYCOLYTI... -

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Basic information

Entry
Database: PDB / ID: 1dqr
TitleCRYSTAL STRUCTURE OF RABBIT PHOSPHOGLUCOSE ISOMERASE, A GLYCOLYTIC ENZYME THAT MOONLIGHTS AS NEUROLEUKIN, AUTOCRINE MOTILITY FACTOR, AND DIFFERENTIATION MEDIATOR
ComponentsPHOSPHOGLUCOSE ISOMERASE
KeywordsISOMERASE / alpha-beta sandwich domains / anti-parallel beta sheet / parallel beta sheet
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
6-PHOSPHOGLUCONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBahnson, B.J. / Jeffery, C.J. / Ringe, D. / Petsko, G.A.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator.
Authors: Jeffery, C.J. / Bahnson, B.J. / Chien, W. / Ringe, D. / Petsko, G.A.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)125,9454
Polymers125,3932
Non-polymers5522
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14040 Å2
ΔGint-85 kcal/mol
Surface area36610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.695, 115.272, 271.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a homodimer of subunits A and B

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Components

#1: Protein PHOSPHOGLUCOSE ISOMERASE


Mass: 62696.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: Q9N1E2, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13% PEG 8000, 250 mM magnesium acetate, 100 mM sodium cacodylate, 5 mM 6-phosphogluconate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 %PEG80001reservoir
2250 mMmagnesium acetate1reservoir
3100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. all: 41256 / Num. obs: 41256 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.4
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.128 / Num. unique all: 3981 / % possible all: 90
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameClassification
CNSrefinement
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→35 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4152 -RANDOM 10%
Rwork0.212 ---
all0.211 41256 --
obs0.211 41256 90.9 %-
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8790 0 34 370 9194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg23
X-RAY DIFFRACTIONc_torsion_impr_deg0.88
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS

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