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- PDB-1kzh: Structure of a pyrophosphate-dependent phosphofructokinase from t... -

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Basic information

Entry
Database: PDB / ID: 1kzh
TitleStructure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi
Componentsphosphofructokinase
KeywordsTRANSFERASE / phosphofructokinase / pyrophosphate / phosphotransferase / spirochete / borrelia burgdorferi
Function / homology
Function and homology information


diphosphate-fructose-6-phosphate 1-phosphotransferase / diphosphate-fructose-6-phosphate 1-phosphotransferase activity / 6-phosphofructokinase activity / fructose 6-phosphate metabolic process / response to glucose / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphofructokinase; domain 3 / Pyrophosphate-dependent phosphofructokinase PfpB / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Arc Repressor Mutant, subunit A / Rossmann fold ...Phosphofructokinase; domain 3 / Pyrophosphate-dependent phosphofructokinase PfpB / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pyrophosphate--fructose 6-phosphate 1-phosphotransferase / Pyrophosphate--fructose 6-phosphate 1-phosphotransferase
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.55 Å
AuthorsMoore, S.A. / Ronimus, R.S. / Roberson, R.S. / Morgan, H.W.
CitationJournal: Structure / Year: 2002
Title: The structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi.
Authors: Moore, S.A. / Ronimus, R.S. / Roberson, R.S. / Morgan, H.W.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 6, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity_name_com / entity_src_gen / reflns / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_source.type / _entity_name_com.name ..._diffrn_source.type / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _reflns.d_resolution_low / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.5Mar 13, 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: phosphofructokinase
B: phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,87210
Polymers125,1042
Non-polymers7698
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-154 kcal/mol
Surface area38370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.098, 97.926, 148.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein phosphofructokinase / Pyrophosphate--fructose 6-phosphate 1-phosphotransferase


Mass: 62551.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB0020 / Plasmid: pProEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: A0A0H3C4C8, UniProt: P70826*PLUS, diphosphate-fructose-6-phosphate 1-phosphotransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M Ammonium Sulphate, 0.1M Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mM11MgCl2
22 mMpyrophosphate11pH7.0
35.0 mg/mlprotein11
42 Mammonium sulfate12
5100 mMTris12pH8.0

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 10, 2001 / Details: Microfocus capillary optics
RadiationMonochromator: microfocus capillary optics, unfiltered / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→100 Å / Num. all: 41099 / Num. obs: 39787 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.4
Reflection shellResolution: 2.55→2.67 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4976 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.334

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Processing

Software
NameVersionClassification
MLPHARESIGMAAphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
SIGMAAphasing
RefinementMethod to determine structure: MIR / Resolution: 2.55→100 Å
Isotropic thermal model: Restrained individual atomic B-factors
Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3320 10 %Random
Rwork0.203 ---
all-41099 --
obs-39787 96.8 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.55→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 40 136 8512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg0.98
LS refinement shellResolution: 2.55→5 Å
RfactorNum. reflection% reflection
Rfree0.243 3995 10 %
Rwork0.203 --
obs-39787 96.8 %
Refinement
*PLUS
Lowest resolution: 100 Å / Num. reflection obs: 39764 / Num. reflection Rfree: 3995 / % reflection Rfree: 9.7 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.243 / Rfactor Rwork: 0.203 / Rfactor obs: 0.203

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