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- PDB-1q50: Phosphoglucose isomerase from Leishmania mexicana. -

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Basic information

Entry
Database: PDB / ID: 1q50
TitlePhosphoglucose isomerase from Leishmania mexicana.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE
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, 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 speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCordeiro, A.T. / Michels, P.A.M. / Delboni, L.F. / Thiemann, O.H.
CitationJournal: EUR.J.BIOCHEM. / Year: 2004
Title: The crystal structure of glucose-6-phosphate isomerase from leishmania mexicana reveals novel active site features
Authors: Cordeiro, A.T. / Michels, P.A.M. / Delboni, L.F. / Thiemann, O.H.
History
DepositionAug 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)62,4521
Polymers62,4521
Non-polymers00
Water3,891216
1
A: Glucose-6-phosphate isomerase

A: Glucose-6-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)124,9032
Polymers124,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area10240 Å2
ΔGint-63 kcal/mol
Surface area38790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.744, 85.744, 350.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Detailshomodimer in the asymmetric unit

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Components

#1: Protein Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 62451.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: PGI / Production host: Escherichia coli (E. coli) / References: UniProt: P42861, glucose-6-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 6K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Nov 30, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 24333 / Num. obs: 24333 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
REFMAC5.1.09refinement
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.206 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 1181 4.9 %RANDOM
Rwork0.19519 ---
obs0.19787 23091 98.74 %-
all-44509 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.936 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 0 216 4603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0214444
X-RAY DIFFRACTIONr_bond_other_d0.0020.023891
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9266029
X-RAY DIFFRACTIONr_angle_other_deg1.01739011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00324.554213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20515725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7531523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025043
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02919
X-RAY DIFFRACTIONr_nbd_refined0.2340.21084
X-RAY DIFFRACTIONr_nbd_other0.260.24463
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.22383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9231.52772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70824459
X-RAY DIFFRACTIONr_scbond_it2.31531672
X-RAY DIFFRACTIONr_scangle_it3.8754.51570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 89
Rwork0.297 1643
Refinement TLS params.Method: refined / Origin x: 20.02 Å / Origin y: 23.388 Å / Origin z: 148.148 Å
111213212223313233
T0.163 Å2-0.101 Å20.0384 Å2-0.1889 Å20.012 Å2--0.0197 Å2
L0.5765 °20.0243 °2-0.0851 °2-1.1756 °20.3268 °2--1.2765 °2
S-0.0358 Å °0.0307 Å °0.0777 Å °0.0617 Å °0.0751 Å °0.1027 Å °0.0504 Å °0.0567 Å °-0.0393 Å °
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2dna-rna.topdna-rna_rep.param
X-RAY DIFFRACTION3water.topwater_rep.param
X-RAY DIFFRACTION4ion.topion.param

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