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- PDB-1nuh: The crystal structure of human phosphoglucose isomerase complexed... -

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Basic information

Entry
Database: PDB / ID: 1nuh
TitleThe crystal structure of human phosphoglucose isomerase complexed with 5-phosphoarabinonate
Componentsglucose phosphate isomerase
KeywordsISOMERASE / ALDOSE-KETOSE ISOMERASE / GLYCOLYSIS ENZYME / NEUROTROPHIC GROWTH FACTOR / CYTOKINE
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 / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / Glycolysis ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / Glycolysis / erythrocyte homeostasis / positive regulation of immunoglobulin production / ciliary membrane / response to testosterone / response to immobilization stress / humoral immune response / mesoderm formation / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / response to progesterone / cytokine activity / glycolytic process / gluconeogenesis / TP53 Regulates Metabolic Genes / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / ficolin-1-rich granule lumen / carbohydrate metabolic process / learning or memory / ubiquitin protein ligase binding / Neutrophil degranulation / negative regulation of apoptotic process / 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
5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / REFINEMENT / Resolution: 2.51 Å
AuthorsDavies, C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: The structure of human phosphoglucose isomerase complexed with a transition-state analogue.
Authors: Davies, C. / Muirhead, H. / Chirgwin, J.
#1: Journal: 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
DepositionJan 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 16, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glucose phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0528
Polymers63,2301
Non-polymers8227
Water1,964109
1
A: glucose phosphate isomerase
hetero molecules

A: glucose phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,10516
Polymers126,4602
Non-polymers1,64514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area15170 Å2
ΔGint-201 kcal/mol
Surface area37050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.400, 94.400, 137.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. The biologically active state is dimeric. The dimer is produced by applying the following operation: y,x,-z

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Components

#1: Protein glucose phosphate isomerase / phosphoglucose isomerase


Mass: 63229.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPI / Plasmid: pET5a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


Type: saccharide / Mass: 246.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 49.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.1 M ammonium sulphate, 100 mM Tris pH 8.5, 5 mM 5-phosphoarabinonate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.5 / Details: Read, J., (2001) J.Mol.Biol., 309, 447.
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.51→94.4 Å / Num. all: 21797 / Num. obs: 21797 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 5.7
Reflection shellResolution: 2.51→2.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2171 / Rsym value: 0.254 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: REFINEMENT
Starting model: PDN ENTRY 1IAT

1iat


Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.872 / SU B: 11.31 / SU ML: 0.256 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.815 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1101 5.1 %RANDOM
Rwork0.214 ---
all0.217 21468 --
obs0.217 21468 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.156 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 45 109 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214570
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.946193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6243554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24615826
X-RAY DIFFRACTIONr_chiral_restr0.1040.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023452
X-RAY DIFFRACTIONr_nbd_refined0.2410.32330
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5360
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.3132
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3480.519
X-RAY DIFFRACTIONr_mcbond_it0.5161.52755
X-RAY DIFFRACTIONr_mcangle_it1.00824439
X-RAY DIFFRACTIONr_scbond_it1.83431815
X-RAY DIFFRACTIONr_scangle_it3.0224.51754
LS refinement shellResolution: 2.51→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.265 91
Rwork0.223 1481
obs-1572
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.48

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