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- PDB-1koj: Crystal structure of rabbit phosphoglucose isomerase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1koj
TitleCrystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / protein - inhibitor 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 / gluconeogenesis / glycolytic process / 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
5-PHOSPHO-D-ARABINOHYDROXAMIC ACID / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArsenieva, D. / Hardre, R. / Salmon, L. / Jeffery, C.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid.
Authors: Arsenieva, D. / Hardre, R. / Salmon, L. / Jeffery, C.J.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9154
Polymers125,3932
Non-polymers5222
Water14,448802
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-74 kcal/mol
Surface area36690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.69, 115.97, 271.85
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein Glucose-6-phosphate isomerase / / E.C.5.3.1.9 / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 62696.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cellular location: CytoplasmicCytoplasm / Tissue: skeletal muscle / References: UniProt: Q9N1E2, glucose-6-phosphate isomerase
#2: Chemical ChemComp-PAN / 5-PHOSPHO-D-ARABINOHYDROXAMIC ACID


Mass: 261.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG 8000, 250mM magnesium acetate, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112-14 %PEG80001reservoir
2250 mMmagnesium acetate1reservoir
3100 mMsodium cacodylate1reservoirpH6.5
415 mg/mlprotein1drop
550 mM1dropKCl
610 mMimidazole1droppH7.5

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Data collection

DiffractionMean temperature: 114 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2000
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 96961 / Num. obs: 96961 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 35.98 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 23.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4 / Num. unique all: 9158 / Rsym value: 0.327 / % possible all: 89
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Num. measured all: 400188 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 89 % / Num. unique obs: 9158 / Rmerge(I) obs: 0.327

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Processing

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

1dqr


Resolution: 1.9→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 9418 10 %random
Rwork0.22 ---
all0.223 94416 --
obs0.223 94416 92.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low5 Å5 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8877 0 32 802 9711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection obs
1.9-1.970.335860100.3078812
1.97-2.050.2999500.2729597
2.05-2.140.2949460.2649725
2.14-2.250.2959550.2589810
2.25-2.390.2959610.2429845
2.39-2.570.2629510.2339756
2.57-2.830.2779820.2349636
2.83-3.230.2569940.2179628
3.23-4.050.2299290.1979021
4.05-120.2278900.1978586
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / Rfactor all: 0.223 / Rfactor obs: 0.22 / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.335 / % reflection Rfree: 10 % / Rfactor Rwork: 0.307 / Rfactor obs: 0.307

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