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- PDB-3q88: Glucose-6-phosphate isomerase from Francisella tularensis complex... -

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Basic information

Entry
Database: PDB / ID: 3q88
TitleGlucose-6-phosphate isomerase from Francisella tularensis complexed with ribose 1,5-bisphosphate.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / STRUCTURAL GENOMICS / FRUCTOSE-6-PHOSPHATE / 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 / 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
ISOPROPYL ALCOHOL / PHOSPHATE ION / 1,5-di-O-phosphono-alpha-D-ribofuranose / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Glucose-6-phosphate isomerase from Francisella tularensis.
Authors: Osipiuk, J. / Maltseva, N. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _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.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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,3627
Polymers61,4661
Non-polymers8966
Water8,701483
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,72414
Polymers122,9332
Non-polymers1,79112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13480 Å2
ΔGint-67 kcal/mol
Surface area38890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.465, 114.465, 84.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 61466.449 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: FTT_1315c, pgi / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NFC4, glucose-6-phosphate isomerase
#2: Sugar ChemComp-RI2 / 1,5-di-O-phosphono-alpha-D-ribofuranose / 1,5-di-O-phosphono-alpha-D-ribose / 1,5-di-O-phosphono-D-ribose / 1,5-di-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 310.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O11P2
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 488 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 52.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Ca(OAc)2, 0.1 M MES buffer, 10% 2-propanol, 0.01 M 5-phospho-alpha-D-ribose 1-diphosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2010
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: 1.7→34 Å / Num. all: 70571 / Num. obs: 70571 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.69 / Num. unique all: 3489 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LJK

3ljk


Resolution: 1.7→33.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.236 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 3521 5 %RANDOM
Rwork0.1462 ---
all0.1476 70373 --
obs0.1476 70373 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.66 Å2 / Biso mean: 27.076 Å2 / Biso min: 6.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.24 Å20 Å2
2---0.47 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 52 483 4847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224865
X-RAY DIFFRACTIONr_bond_other_d0.0010.023302
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9656632
X-RAY DIFFRACTIONr_angle_other_deg0.99438171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26625.612237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04715919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3091514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02941
X-RAY DIFFRACTIONr_mcbond_it0.9821.52889
X-RAY DIFFRACTIONr_mcbond_other0.321.51177
X-RAY DIFFRACTIONr_mcangle_it1.69724698
X-RAY DIFFRACTIONr_scbond_it2.65231976
X-RAY DIFFRACTIONr_scangle_it4.3454.51892
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 279 -
Rwork0.287 4790 -
all-5069 -
obs-5069 98.18 %
Refinement TLS params.Method: refined / Origin x: 46.9428 Å / Origin y: 57.0254 Å / Origin z: 2.7044 Å
111213212223313233
T0.0131 Å2-0.0149 Å2-0.0149 Å2-0.0307 Å20.018 Å2--0.0238 Å2
L0.8022 °2-0.2849 °20.2608 °2-0.527 °2-0.1721 °2--0.4769 °2
S-0.0091 Å °0.0105 Å °0.0389 Å °0.0302 Å °-0.0423 Å °-0.0859 Å °-0.0262 Å °0.0918 Å °0.0515 Å °

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