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- PDB-4a3s: Crystal structure of PFK from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4a3s
TitleCrystal structure of PFK from Bacillus subtilis
Components6-PHOSPHOFRUCTOKINASE
KeywordsTRANSFERASE / GLYCOLYSIS / DEGRADOSOME
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 / canonical glycolysis / ATP binding / metal ion 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
ATP-dependent 6-phosphofructokinase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNewman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A.S. / Harwood, C.R. / Lewis, R.J.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Dissection of the Network of Interactions that Links RNA Processing with Glycolysis in the Bacillus Subtilis Degradosome.
Authors: Newman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A.S. / Harwood, C.R. / Lewis, R.J.
History
DepositionOct 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-PHOSPHOFRUCTOKINASE
B: 6-PHOSPHOFRUCTOKINASE


Theoretical massNumber of molelcules
Total (without water)68,6062
Polymers68,6062
Non-polymers00
Water3,207178
1
A: 6-PHOSPHOFRUCTOKINASE

A: 6-PHOSPHOFRUCTOKINASE

B: 6-PHOSPHOFRUCTOKINASE

B: 6-PHOSPHOFRUCTOKINASE


Theoretical massNumber of molelcules
Total (without water)137,2134
Polymers137,2134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
crystal symmetry operation3_646-x+3/2,y-1/2,-z+11
Buried area12810 Å2
ΔGint-35.4 kcal/mol
Surface area43870 Å2
MethodPISA
2
B: 6-PHOSPHOFRUCTOKINASE

B: 6-PHOSPHOFRUCTOKINASE

A: 6-PHOSPHOFRUCTOKINASE

A: 6-PHOSPHOFRUCTOKINASE


Theoretical massNumber of molelcules
Total (without water)137,2134
Polymers137,2134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_656-x+3/2,y+1/2,-z+11
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area12810 Å2
ΔGint-35.4 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.429, 77.007, 101.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:319 )
211CHAIN B AND (RESSEQ 1:319 )

NCS oper: (Code: given
Matrix: (0.9943, -0.104, -0.02233), (0.1039, 0.9946, -0.00547), (0.02277, 0.003118, 0.9997)
Vector: -40.7363, -48.1891, -54.0556)

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Components

#1: Protein 6-PHOSPHOFRUCTOKINASE / PHOSPHOFRUCTOKINASE / PHOSPHOHEXOKINASE


Mass: 34303.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O34529, 6-phosphofructokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 7 / Details: 100 MM NA HEPES PH 7.0, 12% (W/V) PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9804
DetectorType: ADSC CCD / Detector: CCD / Date: May 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 35387 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 25.83 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.4 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6PFK

6pfk


Resolution: 2.3→45.736 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1815 5.1 %
Rwork0.2293 --
obs0.2317 35379 97.09 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.657 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-14.8124 Å20 Å20 Å2
2---11.7195 Å20 Å2
3----3.0929 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 0 178 4992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014882
X-RAY DIFFRACTIONf_angle_d1.1936576
X-RAY DIFFRACTIONf_dihedral_angle_d18.431816
X-RAY DIFFRACTIONf_chiral_restr0.077748
X-RAY DIFFRACTIONf_plane_restr0.003854
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2407X-RAY DIFFRACTIONPOSITIONAL
12B2407X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.32911040.27952051X-RAY DIFFRACTION78
2.3622-2.43170.35711200.27852321X-RAY DIFFRACTION88
2.4317-2.51020.33261530.26532494X-RAY DIFFRACTION96
2.5102-2.59990.3231250.24882656X-RAY DIFFRACTION100
2.5999-2.7040.29991330.23242611X-RAY DIFFRACTION100
2.704-2.8270.2811690.2332615X-RAY DIFFRACTION100
2.827-2.9760.32651290.23132662X-RAY DIFFRACTION100
2.976-3.16240.30261490.24322611X-RAY DIFFRACTION100
3.1624-3.40650.26181370.24582672X-RAY DIFFRACTION100
3.4065-3.74920.25041340.2282655X-RAY DIFFRACTION100
3.7492-4.29140.2811450.21462699X-RAY DIFFRACTION100
4.2914-5.40530.23691660.20262680X-RAY DIFFRACTION100
5.4053-45.74480.22791510.20652837X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0806-0.06920.01670.11120.02670.0374-0.014-0.0367-0.0981-0.0755-0.0019-0.14450.01770.02390.01890.2467-0.00930.0332-0.0680.07510.113268.335313.466932.3928
20.0080.0064-0.00320.00620.01080.02870.01450.0010.0107-0.00020.0007-0.00230.0327-0.0573-0.02250.0063-0.0186-0.02530.09880.03460.0667.008732.976336.0723
30.0126-0.0032-0.00420.0122-0.01550.0244-0.0069-0.02230.00790.01320.0164-0.0551-0.0179-0.01910.02020.0361-0.0316-0.05390.0790.00450.093564.149946.175142.6662
40.09220.09290.02630.1364-0.0190.1805-0.0881-0.04330.05780.0043-0.0627-0.0775-0.0735-0.041-0.40770.0284-0.0529-0.0097-0.10870.01080.07466.723840.591539.1761
50.02160.0117-0.00380.01610.00620.0083-0.00830.0134-0.0204-0.0010.0068-0.009-0.0150.00940.01130.0622-0.0371-0.05630.07430.02130.099973.225350.558238.512
60.0313-0.00520.00710.11270.00820.0557-0.0534-0.1180.00770.1114-0.0176-0.04-0.0959-0.0013-0.26370.34480.0473-0.2306-0.18660.1876-0.0715116.829650.257183.6568
70.01330.01610.00870.01830.0120.01040.0896-0.0034-0.06470.06030.0368-0.01550.10760.01720.14760.3435-0-0.26420.08520.04460.1725117.624269.797987.2393
80.04470.02150.01360.03030.01820.0143-0.0258-0.09750.08590.1221-0.0251-0.0307-0.0410.00380.01680.6595-0.0614-0.15550.0495-0.07270.1617112.57686.034595.5044
90.00120.0010.00440.00190.00090.00230.006-0.0020.01160.00460.0165-0.01070.0044-0.00020.01650.17350.0595-0.2249-0.08710.05830.1912130.34562.207781.5652
100.030.01660.03050.00970.01240.0635-0.064-0.00720.04560.0579-0.01250.0039-0.0396-0.01950.04190.4816-0.0418-0.08380.261-0.05250.3272124.771589.393688.7259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:103)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 104:161)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 162:197)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 198:302)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 303:319)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1:103)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 104:161)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 162:261)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 262:305)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 306:319)

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