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- PDB-5xz9: Crystal Structure of Phosphofructokinase from Staphylococcus aure... -

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Basic information

Entry
Database: PDB / ID: 5xz9
TitleCrystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate, the ATP analogue
ComponentsATP-dependent 6-phosphofructokinase
KeywordsTRANSFERASE / Phosphofructokinase / Staphylococcus aureus
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
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent 6-phosphofructokinase / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, C.L. / Tian, T. / Zang, J.Y.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Insights into the Regulation of Staphylococcus aureus Phosphofructokinase by Tetramer-Dimer Conversion.
Authors: Tian, T. / Wang, C.L. / Wu, M.H. / Zhang, X. / Zang, J.Y.
History
DepositionJul 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5543
Polymers35,9551
Non-polymers5992
Water1,47782
1
A: ATP-dependent 6-phosphofructokinase
hetero molecules

A: ATP-dependent 6-phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1086
Polymers71,9092
Non-polymers1,1994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5330 Å2
ΔGint-17 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.746, 36.790, 89.800
Angle α, β, γ (deg.)90.00, 123.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ATP-dependent 6-phosphofructokinase / Phosphofructokinase / Phosphohexokinase


Mass: 35954.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: pfkA, SAOUHSC_01807 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FXM8, UniProt: P99165*PLUS, 6-phosphofructokinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 30% MPD, 0.5M Ammonium sulfate, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→74.61 Å / Num. obs: 22161 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1627 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XOE

5xoe


Resolution: 2→74.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.317 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24797 1091 4.9 %RANDOM
Rwork0.2042 ---
obs0.20633 21068 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20.28 Å2
2---1.38 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2→74.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 37 82 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192471
X-RAY DIFFRACTIONr_bond_other_d0.0070.022374
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.9823342
X-RAY DIFFRACTIONr_angle_other_deg1.11935452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83324.951103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04115424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3081514
X-RAY DIFFRACTIONr_chiral_restr0.1180.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022815
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5232.5781287
X-RAY DIFFRACTIONr_mcbond_other2.5132.5771286
X-RAY DIFFRACTIONr_mcangle_it3.7133.851607
X-RAY DIFFRACTIONr_mcangle_other3.7123.851608
X-RAY DIFFRACTIONr_scbond_it3.5273.0111184
X-RAY DIFFRACTIONr_scbond_other3.5263.0111184
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4884.3661736
X-RAY DIFFRACTIONr_long_range_B_refined6.96321.142792
X-RAY DIFFRACTIONr_long_range_B_other6.96321.1392792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 80 -
Rwork0.293 1544 -
obs--99.94 %

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