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- PDB-1c7r: THE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE/AUTOCRINE MOTIL... -

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Basic information

Entry
Database: PDB / ID: 1c7r
TitleTHE CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE/AUTOCRINE MOTILITY FACTOR/NEUROLEUKIN COMPLEXED WITH ITS CARBOHYDRATE PHOSPHATE INHIBITORS AND ITS SUBSTRATE RECOGNITION MECHANISM
ComponentsPHOSPHOGLUCOSE ISOMERASE
KeywordsISOMERASE / PHOSPHOGLUCOSE ISOMERASE/AUTOCRINE MOTILITY FACTOR/ NEUROLEUKIN
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 / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-PHOSPHOARABINONIC ACID / Glucose-6-phosphate isomerase 2
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChou, C.-C. / Meng, M. / Sun, Y.-J. / Hsiao, C.-D.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of phosphoglucose isomerase/autocrine motility factor/neuroleukin complexed with its carbohydrate phosphate inhibitors suggests its substrate/receptor recognition.
Authors: Chou, C.C. / Sun, Y.J. / Meng, M. / Hsiao, C.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The Crystal Structure of a Multifunctional Protein: Phosphoglucose Isomerase/Autocrine Motility Factor/ Neuroleukin
Authors: Sun, Y.-J. / Chou, C.-C. / Chen, W.-S. / Wu, R.-T. / Meng, M. / Hsiao, C.-D.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4492
Polymers50,2031
Non-polymers2461
Water1,69394
1
A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules

A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8984
Polymers100,4062
Non-polymers4922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10970 Å2
ΔGint-69 kcal/mol
Surface area28910 Å2
MethodPISA
2
A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules

A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules

A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules

A: PHOSPHOGLUCOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,7958
Polymers200,8114
Non-polymers9844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)74.800, 94.710, 171.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PHOSPHOGLUCOSE ISOMERASE


Mass: 50202.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cellular location: CYTOPLASM / Plasmid: PFDI22 / Production host: Escherichia coli (E. coli) / Strain (production host): DF2145 / References: UniProt: P13376, glucose-6-phosphate isomerase
#2: Sugar ChemComp-PA5 / 5-PHOSPHOARABINONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.07 Å3/Da / Density % sol: 59.61 %
Crystal growpH: 7 / Details: 0.1M HEPES PH 7.5, 0.8M K, NA TARTRATE
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.05 mM5PA1drop
350 mMphosphate1drop
40.4 Mammonium dihydrogen phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→38.97 Å / Num. obs: 21464 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.08 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Num. measured all: 87547
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.615

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PGI

2pgi


Resolution: 2.5→38.97 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1825 9.9 %RANDOM
Rwork0.215 ---
obs0.215 18434 95.2 %-
Displacement parametersBiso mean: 32.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 15 94 3537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.52
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 204 8.5 %
Rwork0.271 2207 -
obs--89.6 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 2 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.52
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.297 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.271

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