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- PDB-1u2x: Crystal Structure of a Hypothetical ADP-dependent Phosphofructoki... -

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Basic information

Entry
Database: PDB / ID: 1u2x
TitleCrystal Structure of a Hypothetical ADP-dependent Phosphofructokinase from Pyrococcus horikoshii OT3
ComponentsADP-specific phosphofructokinase
KeywordsTRANSFERASE / ADP-Pfk / Pyrococcus / Midwest Center for Structural Genomics / APC5054 / protein structure initiative / PSI / MCSG
Function / homology
Function and homology information


ADP-specific phosphofructokinase / ADP-specific phosphofructokinase activity / phosphofructokinase activity / fructose metabolic process / glycolytic process / magnesium ion binding / cytoplasm
Similarity search - Function
ADP-specific phosphofructokinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...ADP-specific phosphofructokinase, archaeal / Adenosine kinase, small domain - #20 / ADP-specific phosphofructokinase/glucokinase, archaeal / ADP-specific phosphofructokinase/glucokinase / ADP-specific Phosphofructokinase/Glucokinase conserved region / ADP-dependent kinase (ADPK) domain profile. / Adenosine kinase, small domain / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADP-specific phosphofructokinase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWong, A.H.Y. / Jia, Z. / Skarina, T. / Walker, J.R. / Arrowsmith, C. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: ADP-dependent 6-phosphofructokinase from Pyrococcus horikoshii OT3: structure determination and biochemical characterization of PH1645.
Authors: Currie, M.A. / Merino, F. / Skarina, T. / Wong, A.H. / Singer, A. / Brown, G. / Savchenko, A. / Caniuguir, A. / Guixe, V. / Yakunin, A.F. / Jia, Z.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 17, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-specific phosphofructokinase
B: ADP-specific phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9305
Polymers109,6412
Non-polymers2883
Water14,628812
1
A: ADP-specific phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9172
Polymers54,8211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-specific phosphofructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0133
Polymers54,8211
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.065, 99.932, 82.581
Angle α, β, γ (deg.)90.00, 110.38, 90.00
Int Tables number4
Space group name H-MP1211
DetailsEach single molecule is the functional biological unit.

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Components

#1: Protein ADP-specific phosphofructokinase / / ADP-dependent phosphofructokinase / ADP-Pfk


Mass: 54820.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O59355, ADP-specific phosphofructokinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.56 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG4000, 0.1M Tris-HCl, 0.2M LiSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.96396, 0.97918, 0.97943
DetectorType: SBC-3 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.963961
20.979181
30.979431
ReflectionResolution: 2→50 Å / Num. all: 69682 / Num. obs: 69682 / % possible obs: 99.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Rsym value: 0.057 / Net I/σ(I): 21
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.57 / Num. unique all: 6913 / Rsym value: 0.343 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→39.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.231 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.162
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: The structure was refined also with CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22592 3508 5 %RANDOM
Rwork0.17418 ---
all0.199 65970 --
obs0.17678 65970 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7316 0 15 812 8143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0227470
X-RAY DIFFRACTIONr_bond_other_d0.0030.027014
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.97710076
X-RAY DIFFRACTIONr_angle_other_deg0.977316290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995898
X-RAY DIFFRACTIONr_chiral_restr0.1280.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028194
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021558
X-RAY DIFFRACTIONr_nbd_refined0.2330.21717
X-RAY DIFFRACTIONr_nbd_other0.2540.28424
X-RAY DIFFRACTIONr_nbtor_other0.0910.24489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2560
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3380.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.241
X-RAY DIFFRACTIONr_mcbond_it1.3771.54482
X-RAY DIFFRACTIONr_mcangle_it2.45927264
X-RAY DIFFRACTIONr_scbond_it3.97832988
X-RAY DIFFRACTIONr_scangle_it6.4434.52812
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 239
Rwork0.226 4663

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