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- PDB-3drw: Crystal Structure of a Phosphofructokinase from Pyrococcus horiko... -

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Basic information

Entry
Database: PDB / ID: 3drw
TitleCrystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP
ComponentsADP-specific phosphofructokinase
KeywordsTRANSFERASE / 6-phosphofructokinase / Pyrococcus horikoshii / AMP / ADP / Glycolysis / Kinase / Magnesium / Metal-binding / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ADP-specific phosphofructokinase / ADP-specific phosphofructokinase activity / phosphofructokinase activity / fructose metabolic process / glycolytic process / magnesium ion binding / cytoplasm
Similarity search - Function
ADP-specific phosphofructokinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...ADP-specific phosphofructokinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADP-specific phosphofructokinase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSinger, A.U. / Skarina, T. / Kochinyan, S. / Brown, G. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. / Jia, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: ADP-dependent 6-phosphofructokinase from Pyrococcus horikoshii OT3: structure determination and biochemical characterization of PH1645.
Authors: Currie, M.A. / Merino, F. / Skarina, T. / Wong, A.H. / Singer, A. / Brown, G. / Savchenko, A. / Caniuguir, A. / Guixe, V. / Yakunin, A.F. / Jia, Z.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: ADP-specific phosphofructokinase
B: ADP-specific phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7316
Polymers108,9912
Non-polymers7404
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-23 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.464, 104.190, 70.844
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ADP-specific phosphofructokinase / / ADP-dependent phosphofructokinase / ADP-Pfk


Mass: 54495.328 Da / Num. of mol.: 2 / Fragment: phosphofructokinase / Mutation: D17A
Source method: isolated from a genetically manipulated source
Details: no cleavage of N-terminal 6-His tag / Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: pfkC, PH1645 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O59355, ADP-specific phosphofructokinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M Lithium Citrate plus 5 mM ADP Cryoprotected in N-paratone oil., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2007 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 75838 / Num. obs: 74815 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6856 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U2X molecule A

1u2x


Resolution: 1.9→41.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.497 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 3770 5 %RANDOM
Rwork0.17161 ---
obs0.17426 71005 98.27 %-
all-74775 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.03 Å2
2--0.1 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7379 0 48 576 8003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.81.98910267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5425915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10723.579366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.637151401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3771566
X-RAY DIFFRACTIONr_chiral_restr0.1650.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025711
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.23544
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.25297
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2504
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.2108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0821.54550
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99127376
X-RAY DIFFRACTIONr_scbond_it3.54533108
X-RAY DIFFRACTIONr_scangle_it5.9174.52890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 224 -
Rwork0.21 4513 -
obs-4737 85.03 %

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