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- PDB-4rh3: AMPPCP-bound structure of human platelet phosphofructokinase in a... -

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Basic information

Entry
Database: PDB / ID: 4rh3
TitleAMPPCP-bound structure of human platelet phosphofructokinase in an R-state, crystal form II
ComponentsATP-dependent 6-phosphofructokinase, platelet type
KeywordsTRANSFERASE / Phosphohexokinase
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 / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding ...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 / Glycolysis / cellular response to leukemia inhibitory factor / cadherin binding / protein-containing complex binding / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
ATP-dependent 6-phosphofructokinase, vertebrate-type / ATP-dependent 6-phosphofructokinase, eukaryotic-type / Phosphofructokinase domain / Phosphofructokinase, conserved site / Phosphofructokinase signature. / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 ...ATP-dependent 6-phosphofructokinase, vertebrate-type / ATP-dependent 6-phosphofructokinase, eukaryotic-type / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / PHOSPHATE ION / ATP-dependent 6-phosphofructokinase, platelet type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 4WLO / molecular replacement / Resolution: 3.02 Å
AuthorsKloos, M.
CitationJournal: Biochem.J. / Year: 2015
Title: Crystal structure of human platelet phosphofructokinase-1 locked in an activated conformation.
Authors: Kloos, M. / Bruser, A. / Kirchberger, J. / Schoneberg, T. / Strater, N.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: ATP-dependent 6-phosphofructokinase, platelet type
B: ATP-dependent 6-phosphofructokinase, platelet type
C: ATP-dependent 6-phosphofructokinase, platelet type
D: ATP-dependent 6-phosphofructokinase, platelet type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,13315
Polymers324,4474
Non-polymers2,68611
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-dependent 6-phosphofructokinase, platelet type
B: ATP-dependent 6-phosphofructokinase, platelet type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,6148
Polymers162,2242
Non-polymers1,3906
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-42 kcal/mol
Surface area52120 Å2
MethodPISA
3
C: ATP-dependent 6-phosphofructokinase, platelet type
D: ATP-dependent 6-phosphofructokinase, platelet type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,5197
Polymers162,2242
Non-polymers1,2955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-33 kcal/mol
Surface area52460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.911, 132.911, 397.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 25 - 762 / Label seq-ID: 6 - 743

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
ATP-dependent 6-phosphofructokinase, platelet type / ATP-PFK / PFK-P / 6-phosphofructokinase type C / Phosphofructo-1-kinase isozyme C / PFK-C / Phosphohexokinase


Mass: 81111.844 Da / Num. of mol.: 4 / Fragment: UNP residues 26-762
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFKF, PFKP / Plasmid: pET51b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q01813, 6-phosphofructokinase
#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4

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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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0,1 M MES pH 6.0 23% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2014
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.511
11-h,-k,l20.489
ReflectionResolution: 3.02→50 Å / Num. obs: 80705 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.184 / Net I/σ(I): 12.32
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.02-3.20.0112.02199.6
3.2-3.420.0113.411100
3.42-3.70.0115.561100
3.7-4.050.0119.051100
4.05-4.520.01114.381100
4.52-5.210.01118.821100
5.21-6.360.01119.551100
6.36-8.920.01130.361100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å46.9 Å
Translation4 Å46.9 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MxCuBEdata collection
RefinementMethod to determine structure: 4WLO / Resolution: 3.02→46.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.558 / SU ML: 0.154 / SU R Cruickshank DPI: 0.0545 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 4149 5.1 %RANDOM
Rwork0.14626 ---
obs0.14834 76555 99.92 %-
all-80704 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.049 Å2
Baniso -1Baniso -2Baniso -3
1-15.38 Å20 Å20 Å2
2--15.38 Å20 Å2
3----30.75 Å2
Refinement stepCycle: LAST / Resolution: 3.02→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22328 0 159 0 22487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01922844
X-RAY DIFFRACTIONr_bond_other_d0.0070.0222072
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.95830894
X-RAY DIFFRACTIONr_angle_other_deg1.113350624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73952916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89423.968988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.429153972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.55715176
X-RAY DIFFRACTIONr_chiral_restr0.0770.23488
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0226256
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025176
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_it6.6286.69211688
X-RAY DIFFRACTIONr_mcbond_other6.6286.69211687
X-RAY DIFFRACTIONr_mcangle_it10.03910.0314596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.5267.08911156
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A459030.06
12B459030.06
21A464940.04
22C464940.04
31A459870.06
32D459870.06
41B460150.06
42C460150.06
51B466170.04
52D466170.04
61C460040.06
62D460040.06
LS refinement shellResolution: 3.021→3.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 286 -
Rwork0.209 5502 -
obs--98.91 %
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)
10.0461-0.1062-0.02030.3397-0.0240.1656-0.0415-0.01430.00530.0240.0334-0.02570.0463-0.02890.00820.09780.00080.03950.0405-0.05050.101548.3057213.9626427.0056
20.12380.0205-0.1330.12650.02670.3155-0.0513-0.04370.0462-0.0360.0459-0.03020.01960.08450.00540.07030.00420.02350.0711-0.03590.116469.3597237.0114409.5375
30.1188-0.1333-0.11570.33630.01890.21920.0007-0.03070.0089-0.06080.00160.0387-0.0163-0-0.00240.08850.0624-0.0410.0744-0.06570.086711.4913276.9311436.0555
40.08240.0123-0.00060.03620.13340.5629-0.0565-0.0464-0.0224-0.04320.0168-0.006-0.16450.04640.03970.17870.0455-0.03190.0771-0.03410.062340.8418282.642456.2848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 762
2X-RAY DIFFRACTION1A800 - 801
3X-RAY DIFFRACTION1B801
4X-RAY DIFFRACTION2B25 - 762
5X-RAY DIFFRACTION2A802
6X-RAY DIFFRACTION2B802 - 803
7X-RAY DIFFRACTION3C25 - 762
8X-RAY DIFFRACTION3C800 - 801
9X-RAY DIFFRACTION4D25 - 762
10X-RAY DIFFRACTION4C802
11X-RAY DIFFRACTION4D800 - 801

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