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- PDB-5xoe: Crystal Structure of the apo Staphylococcus aureus phosphofructokinase -

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Basic information

Entry
Database: PDB / ID: 5xoe
TitleCrystal Structure of the apo Staphylococcus aureus phosphofructokinase
ComponentsATP-dependent 6-phosphofructokinase
KeywordsTRANSFERASE / Staphylococcus aureus / phosphofructokinase
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 / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, prokaryotic-type / ATP-dependent 6-phosphofructokinase, prokaryotic / 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
ATP-dependent 6-phosphofructokinase / ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsWang, C. / Tian, T. / Zang, J.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Insights into the Regulation of Staphylococcus aureus Phosphofructokinase by Tetramer-Dimer Conversion.
Authors: Tian, T. / Wang, C. / Wu, M. / Zhang, X. / Zang, J.
History
DepositionMay 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref / struct_ref_seq
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
Revision 1.3Nov 22, 2023Group: 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
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


Theoretical massNumber of molelcules
Total (without water)34,8841
Polymers34,8841
Non-polymers00
Water905
1
A: ATP-dependent 6-phosphofructokinase

A: ATP-dependent 6-phosphofructokinase


Theoretical massNumber of molelcules
Total (without water)69,7672
Polymers69,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3310 Å2
ΔGint-11 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.230, 36.949, 87.810
Angle α, β, γ (deg.)90.00, 123.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34883.586 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: Q2FXM8, UniProt: Q2YTE2*PLUS, 6-phosphofructokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 4000, 0.1M MES PH 6.0, 0.15M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.98→73.39 Å / Num. obs: 6551 / % possible obs: 99.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 340 / % possible all: 98.6

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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: 3U39

3u39


Resolution: 2.98→73.39 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.814 / SU B: 22.287 / SU ML: 0.413 / Cross valid method: THROUGHOUT / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31104 309 4.7 %RANDOM
Rwork0.23299 ---
obs0.23646 6240 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.816 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å2-0 Å2-1.41 Å2
2---0.38 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.98→73.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 0 5 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192432
X-RAY DIFFRACTIONr_bond_other_d0.0070.022375
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9653278
X-RAY DIFFRACTIONr_angle_other_deg1.02535456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43424.717106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.71715435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4171516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02527
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_it3.6773.9391270
X-RAY DIFFRACTIONr_mcbond_other3.6713.9381269
X-RAY DIFFRACTIONr_mcangle_it5.8285.9061584
X-RAY DIFFRACTIONr_mcangle_other5.8265.9071585
X-RAY DIFFRACTIONr_scbond_it6.5763.8581162
X-RAY DIFFRACTIONr_scbond_other6.5733.8591163
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1325.771695
X-RAY DIFFRACTIONr_long_range_B_refined11.21229.342693
X-RAY DIFFRACTIONr_long_range_B_other11.21329.3482694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.982→3.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 30 -
Rwork0.265 448 -
obs--94.28 %

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