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- PDB-3o8l: Structure of phosphofructokinase from rabbit skeletal muscle -

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Basic information

Entry
Database: PDB / ID: 3o8l
TitleStructure of phosphofructokinase from rabbit skeletal muscle
Components6-phosphofructokinase, muscle typePhosphofructokinase 1
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


6-phosphofructokinase / 6-phosphofructokinase activity / fructose 6-phosphate metabolic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
ATP-dependent 6-phosphofructokinase, vertebrate-type / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, vertebrate-type / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / ATP-dependent 6-phosphofructokinase, muscle type
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBanaszak, K. / Chang, S.H. / Rypniewski, W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structures of Eukaryotic Phosphofructokinases from Baker's Yeast and Rabbit Skeletal Muscle.
Authors: Banaszak, K. / Mechin, I. / Obmolova, G. / Oldham, M. / Chang, S.H. / Ruiz, T. / Radermacher, M. / Kopperschlager, G. / Rypniewski, W.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphofructokinase, muscle type
B: 6-phosphofructokinase, muscle type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,99114
Polymers166,5382
Non-polymers3,45312
Water0
1
A: 6-phosphofructokinase, muscle type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9967
Polymers83,2691
Non-polymers1,7266
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6-phosphofructokinase, muscle type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9967
Polymers83,2691
Non-polymers1,7266
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.684, 163.684, 356.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe molecule is active as a tetramer, but applying crystal symmetry does not generate a full tetramer.

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Components

#1: Protein 6-phosphofructokinase, muscle type / Phosphofructokinase 1 / Phosphofructokinase 1 / Phosphohexokinase / Phosphofructo-1-kinase isozyme A / PFK-A / Phosphofructokinase-M


Mass: 83269.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PFKM / Plasmid: pET5a / Production host: Escherichia coli (E. coli) / Strain (production host): DF1020DE3 / References: UniProt: P00511, 6-phosphofructokinase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4

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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: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 16% PEG 400, 0.1 M MgSO4, 0.1 M acetate buffer pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 3.2→45 Å / Num. all: 47446 / Num. obs: 47446 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rsym value: 0.14 / Net I/σ(I): 17.8
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.879 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O8O

3o8o


Resolution: 3.2→41 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3022 2361 random
Rwork0.2378 --
obs0.2378 47363 -
all-47363 -
Refinement stepCycle: LAST / Resolution: 3.2→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11438 0 208 0 11646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01252
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_deg1.7998
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3adp.param
X-RAY DIFFRACTION4latp.param

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