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- PDB-1jlh: Human Glucose-6-phosphate Isomerase -

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Basic information

Entry
Database: PDB / ID: 1jlh
TitleHuman Glucose-6-phosphate Isomerase
Componentsphosphoglucose isomeraseGlucose-6-phosphate isomerase
KeywordsISOMERASE / glycolysis / glyconeogenesis
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / humoral immune response / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / gluconeogenesis / TP53 Regulates Metabolic Genes / glycolytic process / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / ficolin-1-rich granule lumen / negative regulation of neuron apoptotic process / learning or memory / carbohydrate metabolic process / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCordeiro, A.T.
CitationJournal: BIOCHIM.BIOPHYS.ACTA / Year: 2003
Title: Crystal structure of human phosphoglucose isomerase and analysis of the initial catalytic steps
Authors: Cordeiro, A.T. / Godoi, P.H.C. / Silva, C.H.T.P. / Garratt, R.C. / Oliva, G. / Thiemann, O.H.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: phosphoglucose isomerase
B: phosphoglucose isomerase
C: phosphoglucose isomerase
D: phosphoglucose isomerase


Theoretical massNumber of molelcules
Total (without water)252,9204
Polymers252,9204
Non-polymers00
Water23,2211289
1
A: phosphoglucose isomerase
B: phosphoglucose isomerase


Theoretical massNumber of molelcules
Total (without water)126,4602
Polymers126,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-76 kcal/mol
Surface area36430 Å2
MethodPISA
2
C: phosphoglucose isomerase
D: phosphoglucose isomerase


Theoretical massNumber of molelcules
Total (without water)126,4602
Polymers126,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12700 Å2
ΔGint-75 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.750, 108.021, 271.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
phosphoglucose isomerase / Glucose-6-phosphate isomerase / PGI / GLUCOSE PHOSPHATE ISOMERASE


Mass: 63229.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET29-a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1289 / 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: 2.41 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 10000, 0.1M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: Cordeiro, A.T., (2001) Acta Crystallogr., D57, 592.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
210 %PEG100001reservoir
3100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.545 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.545 Å / Relative weight: 1
ReflectionResolution: 2.1→22.21 Å / Num. all: 138847 / Num. obs: 138362 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 15.5 Å2 / Limit h max: 38 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 129 / Limit l min: 0 / Observed criterion F max: 3704005.62 / Observed criterion F min: 24.9 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 0.399 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.7 % / Num. measured all: 672976
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.4 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQR

1dqr


Resolution: 2.1→22.21 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 6914 5 %RANDOM
Rwork0.197 ---
all-138843 --
obs-138362 99.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.15 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 78.4 Å2 / Biso mean: 26.8 Å2 / Biso min: 9.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--9.87 Å20 Å2
3----7.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.1→22.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17752 0 0 1289 19041
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.6
X-RAY DIFFRACTIONx_torsion_impr_deg0.92
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_improper_angle_d0.92
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obsTotal num. of bins used% reflection obs (%)
2.1-2.230.2811835.20.233215520.0081719917030699.4
2.2-2.310.2248294.80.225162940.0081723317123899.4
2.31-2.460.2128054.70.211163560.0071725917161899.4
2.46-2.640.21386750.213162920.0071720817159899.7
2.64-2.910.2138735.10.213163680.0071726917241899.8
2.91-3.330.2098474.90.208164960.0071736617343899.9
3.33-4.190.18387350.181165790.0061747017452899.9
4.19-22.210.1689105.10.17169430.0061798317853899.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Highest resolution: 2.1 Å

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