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- PDB-1mto: Crystal structure of a Phosphofructokinase mutant from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 1mto
TitleCrystal structure of a Phosphofructokinase mutant from Bacillus stearothermophilus bound with fructose-6-phosphate
Components6-phosphofructokinase
KeywordsTRANSFERASE / phosphofructokinase / fructose-6-phosphate / tryptophan-shift
Function / homology
Function and homology information


6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding ...6-phosphofructokinase complex / 6-phosphofructokinase / 6-phosphofructokinase activity / fructose-6-phosphate binding / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / monosaccharide binding / canonical glycolysis / AMP binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRiley-Lovingshimer, M.R. / Ronning, D.R. / Sacchettini, J.C. / Reinhart, G.D.
CitationJournal: Biochemistry / Year: 2002
Title: Reversible Ligand-Induced Dissociation of a Tryptophan-Shift Mutant of Phosphofructokinase from Bacillus stearothermophilus
Authors: Riley-Lovingshimer, M.R. / Ronning, D.R. / Sacchettini, J.C. / Reinhart, G.D.
History
DepositionSep 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / 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
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphofructokinase
B: 6-phosphofructokinase
C: 6-phosphofructokinase
D: 6-phosphofructokinase
E: 6-phosphofructokinase
F: 6-phosphofructokinase
G: 6-phosphofructokinase
H: 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,42416
Polymers273,3438
Non-polymers2,0818
Water00
1
A: 6-phosphofructokinase
B: 6-phosphofructokinase
C: 6-phosphofructokinase
D: 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7128
Polymers136,6714
Non-polymers1,0414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-46 kcal/mol
Surface area41730 Å2
MethodPISA
2
E: 6-phosphofructokinase
F: 6-phosphofructokinase
G: 6-phosphofructokinase
H: 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7128
Polymers136,6714
Non-polymers1,0414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-36 kcal/mol
Surface area41230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.682, 106.872, 119.588
Angle α, β, γ (deg.)90.00, 113.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
6-phosphofructokinase / Phosphofructokinase / Phosphohexokinase


Mass: 34167.852 Da / Num. of mol.: 8 / Mutation: W179Y,Y164W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: pfk / Production host: Escherichia coli (E. coli) / Strain (production host): DF1020 / References: UniProt: P00512, 6-phosphofructokinase
#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


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 2.368 Å3/Da / Density % sol: 44.5707 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Sodium Cacodylate, Calcium Acetate, Fructose-6-phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %PEG80001reservoir
20.1 Msodium cacodylate1reservoirpH6.5
30.2 Mcalcium acetate1reservoir
41 mMFru-6-P1reservoir
57.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→29.84 Å / Num. obs: 46829 / Observed criterion σ(F): 0
Reflection
*PLUS
Highest resolution: 3.1 Å / % possible obs: 91.6 % / Num. measured all: 106908 / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
% possible obs: 89.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PFK

3pfk


Resolution: 3.2→29.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 190041.81 / Data cutoff high rms absF: 190041.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3676 10.1 %RANDOM
Rwork0.18 ---
all0.189 ---
obs0.189 36572 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.250378 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.17 Å20 Å24.22 Å2
2--4.93 Å20 Å2
3---0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19200 0 128 0 19328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.512.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 562 10.2 %
Rwork0.259 4959 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2F6P.PARF6P.TOP
Refinement
*PLUS
Highest resolution: 3.1 Å / Num. reflection obs: 32894 / Rfactor Rfree: 0.2746 / Rfactor Rwork: 0.1787
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.146
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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