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- PDB-1hox: CRYSTAL STRUCTURE OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 1hox
TitleCRYSTAL STRUCTURE OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH FRUCTOSE-6-PHOSPHATE
ComponentsPHOSPHOGLUCOSE ISOMERASE
KeywordsISOMERASE / EMZYME -SUBSTRATE COMPLEX
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
6-O-phosphono-beta-D-fructofuranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJeffrey, C.J. / Lee, J.H. / Chang, K.Z. / Patel, V.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of rabbit phosphoglucose isomerase complexed with its substrate D-fructose 6-phosphate.
Authors: Lee, J.H. / Chang, K.Z. / Patel, V. / Jeffery, C.J.
History
DepositionDec 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)126,1764
Polymers125,6552
Non-polymers5202
Water15,637868
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-70 kcal/mol
Surface area35910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.438, 119.429, 272.137
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-1118-

HOH

21B-1138-

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: PROTEIN PURIFIED FROM RABBIT SKELETAL MUSCLE / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q9N1E2, glucose-6-phosphate isomerase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, IMIDAZOLE, POTASSIUM CHLORIDE, PHOSPHOGLUCOSE ISOMERASE, D-GLUCOSE-6-PHOSPHATE, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 7.5. VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118-20 mg/mlenzyme1drop
25 mMD-glucose 6-phosphate1drop
310 mMimidazole1drop
450 mM1dropKCl
514.5 %PEG80001reservoir
6250 mMmagnesium acetate1reservoir
7100 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: Jun 12, 1999
RadiationMonochromator: BENT CONICAL SI-MIRROR (RH COATING), BENT CYLINDRICAL GE(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 77413 / Num. obs: 77413 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.08 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 18.47
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.08 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.63 / Num. unique all: 7640 / Rsym value: 0.346 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 315852
Reflection shell
*PLUS
% possible obs: 98.3 % / Num. unique obs: 7640 / Num. measured obs: 31147

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Processing

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

1dqr


Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 7391 9.5 %RANDOM
Rwork0.2174 ---
all0.221 77413 --
obs0.221 77413 93.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8790 0 32 868 9690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0108
X-RAY DIFFRACTIONc_angle_deg1.505
X-RAY DIFFRACTIONc_dihedral_angle_d23.77
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3721 696 -
Rwork0.3474 --
obs-6622 98 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 9.5 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.77
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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