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- PDB-3opy: Crystal structure of Pichia pastoris phosphofructokinase in the T... -

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Basic information

Entry
Database: PDB / ID: 3opy
TitleCrystal structure of Pichia pastoris phosphofructokinase in the T-state
Components
  • 6-phosphofructo-1-kinase alpha-subunit
  • 6-phosphofructo-1-kinase beta-subunit
  • 6-phosphofructo-1-kinase gamma-subunit
KeywordsTRANSFERASE / phosphofructokinase / ATP Binding / Fructose-6-phosphate Binding / Magnesium Binding / Citrate Binding / ADP Binding / Fructose-2 / 6-bisphosphate Binding
Function / homology
Function and homology information


6-phosphofructokinase / 6-phosphofructokinase activity / fructose 6-phosphate metabolic process / glycolytic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 - #90 / Rossmann fold - #11920 / Pichia pastoris 6-phosphofructokinase, gamma subunit / Pichia pastoris 6-phosphofructokinase, gamma subunit superfamily / Phosphofructokinase, N-terminal domain / Phosphofructokinase N-terminal domain yeast / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain ...2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 - #90 / Rossmann fold - #11920 / Pichia pastoris 6-phosphofructokinase, gamma subunit / Pichia pastoris 6-phosphofructokinase, gamma subunit superfamily / Phosphofructokinase, N-terminal domain / Phosphofructokinase N-terminal domain yeast / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ATP-dependent 6-phosphofructokinase subunit gamma / ATP-dependent 6-phosphofructokinase subunit alpha / ATP-dependent 6-phosphofructokinase subunit beta
Similarity search - Component
Biological speciesPichia pastoris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsStrater, N. / Marek, S. / Kuettner, E.B. / Kloos, M. / Keim, A. / Bruser, A. / Kirchberger, J. / Schoneberg, T.
CitationJournal: Faseb J. / Year: 2011
Title: Molecular architecture and structural basis of allosteric regulation of eukaryotic phosphofructokinases.
Authors: Strater, N. / Marek, S. / Kuettner, E.B. / Kloos, M. / Keim, A. / Bruser, A. / Kirchberger, J. / Schoneberg, T.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-phosphofructo-1-kinase alpha-subunit
B: 6-phosphofructo-1-kinase beta-subunit
C: 6-phosphofructo-1-kinase alpha-subunit
D: 6-phosphofructo-1-kinase beta-subunit
E: 6-phosphofructo-1-kinase alpha-subunit
F: 6-phosphofructo-1-kinase beta-subunit
G: 6-phosphofructo-1-kinase alpha-subunit
H: 6-phosphofructo-1-kinase beta-subunit
I: 6-phosphofructo-1-kinase gamma-subunit
J: 6-phosphofructo-1-kinase gamma-subunit
K: 6-phosphofructo-1-kinase gamma-subunit
L: 6-phosphofructo-1-kinase gamma-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,022,78881
Polymers1,014,51512
Non-polymers8,27369
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area92490 Å2
ΔGint-1393 kcal/mol
Surface area305400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.658, 188.303, 231.560
Angle α, β, γ (deg.)90.00, 92.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains a complete biological assembly

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Components

#1: Protein
6-phosphofructo-1-kinase alpha-subunit


Mass: 108929.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pichia pastoris (fungus) / Strain: DSMZ 70382 / References: UniProt: Q8NJU8, 6-phosphofructokinase
#2: Protein
6-phosphofructo-1-kinase beta-subunit


Mass: 103853.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pichia pastoris (fungus) / Strain: DSMZ 70382 / References: UniProt: Q8TGA0, 6-phosphofructokinase
#3: Protein
6-phosphofructo-1-kinase gamma-subunit


Mass: 40845.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pichia pastoris (fungus) / Strain: DSMZ 70382 / References: UniProt: A7MAS3, 6-phosphofructokinase
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.6
Details: 1 microliter of protein + 1 microliter of reservoir using streak seading, protein: 1mg/mL PFK, 10mM imidazol, 5mM mercaptoethanol, 10% glycerol, 10mM ATP, pH 7.0; reservoir: 0.7M ammonia ...Details: 1 microliter of protein + 1 microliter of reservoir using streak seading, protein: 1mg/mL PFK, 10mM imidazol, 5mM mercaptoethanol, 10% glycerol, 10mM ATP, pH 7.0; reservoir: 0.7M ammonia sulfate, 0.1M sodium citrate pH 4.6, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 13, 2009
Details: Double crystal monochromator with 2 sets of mirrors
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.05→29.8 Å / Num. obs: 262877 / % possible obs: 53.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 97.5 % / Biso Wilson estimate: 75.78 Å2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→29.8 Å / Cor.coef. Fo:Fc: 0.8802 / Cor.coef. Fo:Fc free: 0.8458 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 12864 5.03 %RANDOM
Rwork0.2003 ---
all0.247 617625 --
obs0.2019 255838 --
Displacement parametersBiso mean: 68.17 Å2
Baniso -1Baniso -2Baniso -3
1--13.4997 Å20 Å2-1.0224 Å2
2--9.7517 Å20 Å2
3---3.748 Å2
Refine analyzeLuzzati coordinate error obs: 0.529 Å
Refinement stepCycle: LAST / Resolution: 3.05→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64576 0 449 0 65025
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d22308SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes1608HARMONIC2
X-RAY DIFFRACTIONt_gen_planes9720HARMONIC5
X-RAY DIFFRACTIONt_it66060HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion16HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion8988SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact76198SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d66060HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg89582HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion22.51
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2664 947 4.97 %
Rwork0.2266 18092 -
all0.2286 19039 -
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)
10.1884-0.2507-0.95051.6985-1.27511.50760.09760.5690.07720.02-0.1719-0.0845-0.50010.05990.07440.01240.2455-0.03230.25490.2325-0.4385-13.02365.2786-39.4613
20.92480.0872-0.0730.93670.0620.80020.0762-0.07460.03710.0469-0.0119-0.30940.05940.1859-0.0643-0.2620.0181-0.1279-0.1391-0.026-0.1301-5.988-13.069628.5155
30.00030.5938-0.01044.50431.16062.67420.01140.2827-0.6360.1197-0.0197-0.12240.38290.07150.00820.09010.0953-0.02550.0278-0.4054-0.3142-59.8734-23.6023-36.8957
41.4245-0.075-0.30690.7416-0.01130.93930.0390.3377-0.3226-0.1557-0.0729-0.05630.1013-0.03620.0339-0.21440.0683-0.0774-0.2084-0.1365-0.1391-18.9168-30.1707-1.2732
51.61730.3208-0.03651.5585-0.23081.32240.118-0.1977-0.10770.1674-0.04950.32210.1459-0.2966-0.0685-0.2044-0.0969-0.1103-0.1466-0.0904-0.0549-66.8353-37.204428.0454
61.12090.16950.62661.69411.67571.47950.12660.656-0.2439-0.0154-0.23540.30850.6496-0.03030.1088-0.03680.1146-0.02860.344-0.163-0.3482-67.7727-6.5915-39.4107
71.2270.050.16480.9112-0.01480.76390.0768-0.1126-0.0320.1137-0.02890.2712-0.0771-0.2239-0.048-0.25030.00280.0177-0.12210.0484-0.1408-75.068712.805228.2469
81.18661.8078-0.47474.00341.01894.07230.06890.05050.7818-0.07720.03030.2068-0.3755-0.0684-0.09920.10160.18540.06220.07040.3947-0.3369-21.05422.2062-37.2977
91.34750.01690.28770.6512-0.03481.00140.01890.3570.3254-0.101-0.05270.0854-0.080.03240.0339-0.23210.0594-0.0235-0.19870.1283-0.1124-62.00929.4658-1.8076
102.08890.0211-0.23941.3439-0.02091.25340.1029-0.15520.03560.21-0.03-0.2682-0.06750.2664-0.0729-0.2041-0.0857-0.0341-0.15690.0562-0.0763-14.17336.817527.5284
112.28620.5836-0.2720.78190.62161.22810.0698-0.0257-0.1024-0.0438-0.11820.2376-0.1715-0.06980.04840.1071-0.03010.01590.5838-0.1502-0.4291-67.875-6.5488153.8845
120.9355-0.1966-0.15730.5826-0.09050.6734-0.0827-0.1449-0.18260.01430.060.37680.121-0.13980.02260.0543-0.156-0.04690.23440.14410.0641-65.0857-27.157686.2498
133.1180.23950.03494.9612-0.282.87430.02220.0588-0.65910.046-0.1715-0.19060.36390.00460.14920.1666-0.0504-0.08950.28590.332-0.411-13.1608-10.096152.0457
141.33580.0929-0.16770.6740.35120.8167-0.0582-0.6112-0.40570.2253-0.06160.00640.16670.05330.11980.1358-0.0479-0.04980.42630.3468-0.0916-45.8462-35.6323116.4215
152.0003-0.1252-0.12551.321-0.22012.38460.064-0.17840.0617-0.0696-0.001-0.26720.03690.4001-0.0631-0.1669-0.0418-0.1197-0.0210.0575-0.2953-0.0532-20.149586.6654
162.6561-0.01610.65261.3843-0.94451.90450.0505-0.26910.1188-0.0788-0.2799-0.29430.1730.06170.22950.0791-0.0704-0.11140.42580.2369-0.4103-13.56058.6634153.851
170.7834-0.22870.28940.66990.18710.7189-0.1247-0.0880.08590.01420.1752-0.3187-0.15030.0082-0.05040.1364-0.1448-0.0890.1742-0.1085-0.0036-16.11327.782685.7703
182.6263-1.3430.01384.82420.64534.4270.01280.23220.6434-0.0116-0.06560.017-0.35560.0210.05270.22570.00820.07640.2845-0.2312-0.3333-68.49612.5734151.6128
191.14530.31880.23210.6521-0.07160.8645-0.0723-0.42540.23540.1119-0.07360.1072-0.1665-0.31910.14590.1610.0133-0.12590.2989-0.1797-0.1633-35.333237.0371115.6783
201.7423-0.60490.55281.80030.15972.258-0.0366-0.2424-0.06790.00030.0770.42530.0061-0.457-0.0405-0.3275-0.0143-0.05950.1615-0.0253-0.2807-81.229620.853186.5841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|5 - 186}A5 - 186
2X-RAY DIFFRACTION2{A|208 - 989}A208 - 989
3X-RAY DIFFRACTION3{B|5 - 155}B5 - 155
4X-RAY DIFFRACTION4{B|180 - 941}B180 - 941
5X-RAY DIFFRACTION5{I|5 - 351}I5 - 351
6X-RAY DIFFRACTION6{C|5 - 186}C5 - 186
7X-RAY DIFFRACTION7{C|208 - 989}C208 - 989
8X-RAY DIFFRACTION8{D|5 - 155}D5 - 155
9X-RAY DIFFRACTION9{D|180 - 941}D180 - 941
10X-RAY DIFFRACTION10{J|5 - 351}J5 - 351
11X-RAY DIFFRACTION11{E|5 - 186}E5 - 186
12X-RAY DIFFRACTION12{E|208 - 989}E208 - 989
13X-RAY DIFFRACTION13{F|5 - 155}F5 - 155
14X-RAY DIFFRACTION14{F|180 - 941}F180 - 941
15X-RAY DIFFRACTION15{K|5 - 351}K5 - 351
16X-RAY DIFFRACTION16{G|5 - 186}G5 - 186
17X-RAY DIFFRACTION17{G|208 - 989}G208 - 989
18X-RAY DIFFRACTION18{H|5 - 155}H5 - 155
19X-RAY DIFFRACTION19{H|180 - 941}H180 - 941
20X-RAY DIFFRACTION20{L|5 - 351}L5 - 351

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