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- PDB-1t10: Phosphoglucose isomerase from Leishmania mexicana in complex with... -

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Basic information

Entry
Database: PDB / ID: 1t10
TitlePhosphoglucose isomerase from Leishmania mexicana in complex with substrate D-fructose-6-phosphate
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / phosphoglucose isomerase / substrate / D-fructose-6-phosphate
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / gluconeogenesis / glycolytic process / cytoplasm
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
6-O-phosphono-beta-D-fructofuranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesLeishmania mexicana mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCordeiro, A.T. / Thiemann, O.T.
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. / Delboni, L.F. / Thiemann, O.T.
History
DepositionApr 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6222
Polymers67,3621
Non-polymers2601
Water3,243180
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2454
Polymers134,7242
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area11410 Å2
ΔGint-77 kcal/mol
Surface area38240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.129, 85.129, 350.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122
DetailsThe biological unit is a homodimer formed by the 2-fold crystallographic rotation applied chain A in the asymmetric unit

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Components

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


Mass: 67362.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The primary reference points to an incorrect PDB ID, 1Q1I
Source: (gene. exp.) Leishmania mexicana mexicana (eukaryote)
Species: Leishmania mexicana / Strain: mexicana / Gene: PGI / Production host: Escherichia coli (E. coli) / References: UniProt: P42861, glucose-6-phosphate isomerase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose / Fructose 6-phosphate


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.87 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10% PEG 6000, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.35→74.536 Å / Num. all: 32626 / Num. obs: 32626 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 58.58 Å2 / Rsym value: 0.061
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4622 / Rsym value: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
AMoREphasing
REFMAC5.1.09refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→74.53 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.547 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25983 1618 5 %RANDOM
Rwork0.22031 ---
all0.22228 30902 --
obs0.22228 30902 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.35→74.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4355 0 16 180 4551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214463
X-RAY DIFFRACTIONr_bond_other_d0.0030.023974
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9316045
X-RAY DIFFRACTIONr_angle_other_deg0.96839241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22624.528212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.48515755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4851523
X-RAY DIFFRACTIONr_chiral_restr0.0950.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025004
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02914
X-RAY DIFFRACTIONr_nbd_refined0.2390.21161
X-RAY DIFFRACTIONr_nbd_other0.2610.24717
X-RAY DIFFRACTIONr_nbtor_other0.0920.22420
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.2142
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.214
X-RAY DIFFRACTIONr_mcbond_it0.6951.52749
X-RAY DIFFRACTIONr_mcangle_it1.27224421
X-RAY DIFFRACTIONr_scbond_it1.79831714
X-RAY DIFFRACTIONr_scangle_it2.9474.51624
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 110
Rwork0.289 2217
Refinement TLS params.Method: refined / Origin x: 20.22 Å / Origin y: 23.055 Å / Origin z: 147.986 Å
111213212223313233
T0.1718 Å2-0.0197 Å20.0609 Å2-0.2354 Å20.0909 Å2--0.0647 Å2
L0.8227 °20.2177 °2-0.0147 °2-2.0904 °20.4202 °2--1.8039 °2
S-0.0425 Å °0.1928 Å °0.0464 Å °0.3636 Å °0.2442 Å °0.155 Å °0.2068 Å °0.0004 Å °-0.2017 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA49 - 60449 - 604
2X-RAY DIFFRACTION1AA10011001
3X-RAY DIFFRACTION1AA1002 - 11811002 - 1181

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