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- PDB-1iat: CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLUCOSE ISOMERASE/NEUROLEUKIN/A... -

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Basic information

Entry
Database: PDB / ID: 1iat
TitleCRYSTAL STRUCTURE OF HUMAN PHOSPHOGLUCOSE ISOMERASE/NEUROLEUKIN/AUTOCRINE MOTILITY FACTOR/MATURATION FACTOR
ComponentsPHOSPHOGLUCOSE ISOMERASE
KeywordsISOMERASE / glycolysis enzyme/neurotrophic growth factor/cytokine / two alpha/beta domains
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 / cytokine activity / gluconeogenesis / response to progesterone / glycolytic process / TP53 Regulates Metabolic Genes / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / ficolin-1-rich granule lumen / carbohydrate metabolic process / learning or memory / 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
BETA-MERCAPTOETHANOL / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsRead, J.A. / Pearce, J. / Li, X. / Muirhead, H. / Chirgwin, J. / Davies, C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The crystal structure of human phosphoglucose isomerase at 1.6 A resolution: implications for catalytic mechanism, cytokine activity and haemolytic anaemia.
Authors: Read, J. / Pearce, J. / Li, X. / Muirhead, H. / Chirgwin, J. / Davies, C.
History
DepositionMar 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3694
Polymers63,0991
Non-polymers2703
Water10,467581
1
A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules

A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7388
Polymers126,1972
Non-polymers5416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14200 Å2
ΔGint-134 kcal/mol
Surface area37300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.183, 94.183, 136.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

21A-1059-

HOH

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Components

#1: Protein PHOSPHOGLUCOSE ISOMERASE / GLUCOSE-6-PHOSPHATE ISOMERASE / GLUCOSE PHOSPHATE ISOMERASE


Mass: 63098.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPI / Production host: Escherichia coli (E. coli) / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium sulphate, tris-HCl, Na Hepes, beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.6 Mammonium sulfate1reservoir
2100 mMTris1reservoir
315 mMHEPES1drop
42 mMbeta-mercaptoethanol1drop
54 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.62→30 Å / Num. all: 75504 / Num. obs: 75504 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.13 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 30.65
Reflection shellResolution: 1.62→1.69 Å / Redundancy: 4.52 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 7.33 / % possible all: 88.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 88.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PIG MUSCLE PGI (unpublished)

Resolution: 1.62→29.88 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.17 3766 5 %RANDOM
Rwork0.144 ---
all0.1466 70947 --
obs0.1466 70947 95.5 %-
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.62→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4437 0 14 581 5032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it27601.163
X-RAY DIFFRACTIONp_mcangle_it44491.858
X-RAY DIFFRACTIONp_scbond_it17962.772
X-RAY DIFFRACTIONp_scangle_it17194.228
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 231
Rwork0.21 4277
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.59

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