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- PDB-3umo: Crystal structure of the Phosphofructokinase-2 from Escherichia c... -

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Basic information

Entry
Database: PDB / ID: 3umo
TitleCrystal structure of the Phosphofructokinase-2 from Escherichia coli in complex with Potassium
Components6-phosphofructokinase isozyme 2
KeywordsTRANSFERASE / GLYCOLYSIS / PFK / enzyme
Function / homology
Function and homology information


tagatose-6-phosphate kinase activity / 6-phosphofructokinase / 6-phosphofructokinase activity / glycolytic process / DNA damage response / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / ATP-dependent 6-phosphofructokinase isozyme 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.696 Å
AuthorsPereira, H.M. / Caniuguir, A. / Baez, M. / Cabrera, R. / Garratt, R.C. / Babul, J.
CitationJournal: Biophys.J. / Year: 2013
Title: A Ribokinase Family Conserved Monovalent Cation Binding Site Enhances the MgATP-induced Inhibition in E. coli Phosphofructokinase-2
Authors: Baez, M. / Cabrera, R. / Pereira, H.M. / Blanco, A. / Villalobos, P. / Ramirez-Sarmiento, C.A. / Caniuguir, A. / Guixe, V. / Garratt, R.C. / Babul, J.
History
DepositionNov 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 13, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: 6-phosphofructokinase isozyme 2
B: 6-phosphofructokinase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,17812
Polymers64,9742
Non-polymers2,20410
Water10,233568
1
A: 6-phosphofructokinase isozyme 2
B: 6-phosphofructokinase isozyme 2
hetero molecules

A: 6-phosphofructokinase isozyme 2
B: 6-phosphofructokinase isozyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,35624
Polymers129,9484
Non-polymers4,40820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-77 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.812, 88.770, 176.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

21B-504-

HOH

31B-640-

HOH

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Components

#1: Protein 6-phosphofructokinase isozyme 2 / Phosphofructokinase-2


Mass: 32486.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1723, JW5280, PFK2, pfkB / Plasmid: PET21-D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06999, 6-phosphofructokinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2010 / Details: DCM Si(311) and Si(111)
RadiationMonochromator: SI(311) AND SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.696→50 Å / Num. all: 77204 / Num. obs: 76251 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.02 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.06
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.696-1.80.592.045341212064198.1
1.8-1.920.3393.594979411535199.6
1.92-2.080.1886.794897710794199.7
2.08-2.270.11611.23421019818198.8
2.27-2.540.07816.94402118985198.9
2.54-2.930.05624.01333337929198.5
2.93-3.590.03933.33288036728198.3
3.59-5.060.03238.92212185293198.1
5.06-500.02640.58126663105197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
DMphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CQD
Resolution: 1.696→48.967 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.48 / σ(F): 2.02 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 3813 5 %Random
Rwork0.1814 ---
obs0.1828 76249 98.77 %-
all-77204 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.314 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 87.65 Å2 / Biso mean: 30.7992 Å2 / Biso min: 10.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.8126 Å2-0 Å2-0 Å2
2--2.0555 Å2-0 Å2
3----0.2429 Å2
Refinement stepCycle: LAST / Resolution: 1.696→48.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 130 568 5240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114826
X-RAY DIFFRACTIONf_angle_d1.2976606
X-RAY DIFFRACTIONf_chiral_restr0.064776
X-RAY DIFFRACTIONf_plane_restr0.004838
X-RAY DIFFRACTIONf_dihedral_angle_d20.151794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.696-1.71770.33741290.30522454258393
1.7177-1.74030.36971430.297927172860100
1.7403-1.76410.30051390.279126462785100
1.7641-1.78930.29311390.271626392778100
1.7893-1.8160.29471420.264827012843100
1.816-1.84440.29821400.258426562796100
1.8444-1.87460.27841390.23992637277699
1.8746-1.9070.22971440.224627442888100
1.907-1.94160.23971390.20126392778100
1.9416-1.9790.22941430.198827052848100
1.979-2.01940.22851400.196126592799100
2.0194-2.06330.21271410.186626832824100
2.0633-2.11130.20021410.18682679282099
2.1113-2.16410.20011390.17362647278699
2.1641-2.22260.2081400.1762658279899
2.2226-2.2880.24531410.18032670281198
2.288-2.36190.20881400.17872668280899
2.3619-2.44630.21341430.17712706284999
2.4463-2.54420.20881400.17642663280399
2.5442-2.660.21891410.17422680282199
2.66-2.80020.22171410.18292687282899
2.8002-2.97560.21761420.17942688283098
2.9756-3.20530.22511410.18642696283798
3.2053-3.52780.20391440.18312720286498
3.5278-4.03810.18371440.15962749289398
4.0381-5.08670.14461440.13832730287498
5.0867-48.98750.18861540.17612915306998

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