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- PDB-3hno: Crystal Structure of Pyrophosphate-dependent phosphofructokinase ... -

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Basic information

Entry
Database: PDB / ID: 3hno
TitleCrystal Structure of Pyrophosphate-dependent phosphofructokinase from Nitrosospira multiformis. Northeast Structural Genomics Consortium target id NmR42
ComponentsPyrophosphate-dependent phosphofructokinase
KeywordsTRANSFERASE / Pyrophosphate-dependent phosphofructokinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ATP-binding / Kinase / Nucleotide-binding
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 / metal ion binding / cytoplasm
Similarity search - Function
Pyrophosphate--fructose 6-phosphate 1-phosphotransferase, XF0274 / Phosphofructokinase domain / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Pyrophosphate--fructose 6-phosphate 1-phosphotransferase
Similarity search - Component
Biological speciesNitrosospira multiformis ATCC 25196 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeetharaman, J. / Abashidze, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Abashidze, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Pyrophosphate-dependent phosphofructokinase from Nitrosospira multiformis. Northeast Structural Genomics Consortium target id NmR42
Authors: Seetharaman, J. / Abashidze, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Feb 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

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Assembly

Deposited unit
A: Pyrophosphate-dependent phosphofructokinase
B: Pyrophosphate-dependent phosphofructokinase
C: Pyrophosphate-dependent phosphofructokinase
D: Pyrophosphate-dependent phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,5295
Polymers180,4494
Non-polymers801
Water7,945441
1
C: Pyrophosphate-dependent phosphofructokinase
hetero molecules

A: Pyrophosphate-dependent phosphofructokinase


Theoretical massNumber of molelcules
Total (without water)90,3043
Polymers90,2252
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
2
D: Pyrophosphate-dependent phosphofructokinase

B: Pyrophosphate-dependent phosphofructokinase


Theoretical massNumber of molelcules
Total (without water)90,2252
Polymers90,2252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
3
A: Pyrophosphate-dependent phosphofructokinase

C: Pyrophosphate-dependent phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3043
Polymers90,2252
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area5570 Å2
ΔGint-31 kcal/mol
Surface area28630 Å2
MethodPISA
4
B: Pyrophosphate-dependent phosphofructokinase

D: Pyrophosphate-dependent phosphofructokinase


Theoretical massNumber of molelcules
Total (without water)90,2252
Polymers90,2252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area5420 Å2
ΔGint-31 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.895, 89.322, 115.462
Angle α, β, γ (deg.)90.00, 119.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Pyrophosphate-dependent phosphofructokinase


Mass: 45112.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosospira multiformis ATCC 25196 (bacteria)
Gene: Nmul_A0740 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2YB24, diphosphate-fructose-6-phosphate 1-phosphotransferase
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM KBr, 100mM na3citrate, pH 4.5, 18% Peg 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 271192 / Num. obs: 253147 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.054 / Net I/σ(I): 31.4
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 12 / Num. unique all: 12925 / Rsym value: 0.2 / % possible all: 94

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→39.45 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 134698.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 11639 4.9 %RANDOM
Rwork0.216 ---
obs0.216 236816 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3511 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--5.54 Å20 Å21.8 Å2
2--10.59 Å20 Å2
3----5.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11866 0 1 441 12308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 1581 4.7 %
Rwork0.248 31987 -
obs--80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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