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- PDB-3m5p: Glucose-6-phosphate isomerase from Francisella tularensis complex... -

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Basic information

Entry
Database: PDB / ID: 3m5p
TitleGlucose-6-phosphate isomerase from Francisella tularensis complexed with fructose-6-phosphate.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / structural genomics / IDP02733 / glucose-6-phosphate / fructose-6-phosphate. / Cytoplasm / Gluconeogenesis / Glycolysis / Center for Structural Genomics of Infectious Diseases / CSGID
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 / PHOSPHATE ION / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsOsipiuk, J. / Maltseva, N. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of glucose-6-phosphate isomerase from Francisella tularensis complexed with fructose-6-phosphate.
Authors: Osipiuk, J. / Maltseva, N. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 6, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,5937
Polymers61,9351
Non-polymers6576
Water9,062503
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,18514
Polymers123,8712
Non-polymers1,31512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area14560 Å2
ΔGint-117 kcal/mol
Surface area37980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.272, 114.272, 83.723
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsbiological unit is a dimer.

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 61935.395 Da / Num. of mol.: 1 / Mutation: F194L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT1315c, pgi / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NFC4, 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

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Non-polymers , 4 types, 508 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M sodium/potassium phosphate buffer, 35% MPD, 10 mM fructose-6-phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→32.1 Å / Num. all: 76000 / Num. obs: 76000 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.964 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.14 / Num. unique all: 3723 / Χ2: 0.716 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→32.1 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.971 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.099 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16 3810 5 %RANDOM
Rwork0.131 ---
all0.132 75874 --
obs0.132 75874 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.58 Å2 / Biso mean: 17.864 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.35 Å20 Å2
2---0.69 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 45 504 5169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224796
X-RAY DIFFRACTIONr_bond_other_d0.0010.023257
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9636553
X-RAY DIFFRACTIONr_angle_other_deg0.93738075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26825.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2715915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6551515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
X-RAY DIFFRACTIONr_mcbond_it1.3111.52848
X-RAY DIFFRACTIONr_mcbond_other0.4351.51157
X-RAY DIFFRACTIONr_mcangle_it2.04124643
X-RAY DIFFRACTIONr_scbond_it3.4431948
X-RAY DIFFRACTIONr_scangle_it5.0884.51857
X-RAY DIFFRACTIONr_rigid_bond_restr1.41738053
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 290 -
Rwork0.28 5163 -
all-5453 -
obs-5453 98.38 %
Refinement TLS params.Method: refined / Origin x: 46.9613 Å / Origin y: 57.0017 Å / Origin z: 2.5998 Å
111213212223313233
T0.0115 Å2-0.0182 Å2-0.0079 Å2-0.0457 Å20.0144 Å2--0.0196 Å2
L0.925 °2-0.3166 °20.3825 °2-0.6797 °2-0.2677 °2--0.6442 °2
S0.0087 Å °0.0109 Å °0.0276 Å °0.0197 Å °-0.0571 Å °-0.1044 Å °-0.0268 Å °0.1226 Å °0.0485 Å °

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