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- PDB-3ahc: Resting form of Phosphoketolase from Bifidobacterium Breve -

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Basic information

Entry
Database: PDB / ID: 3ahc
TitleResting form of Phosphoketolase from Bifidobacterium Breve
ComponentsXylulose 5-phosphate/fructose 6-phosphate phosphoketolase
KeywordsLYASE / THIAMINE DIPHOSPHATE-DEPENDENT ENZYME / ALPHA-BETA FOLD / HOMODIMER / LIGAND-FREE STRUCTURE
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Aldehyde-lyases / aldehyde-lyase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Probable phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. ...Probable phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. / Rossmann fold - #920 / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Probable phosphoketolase
Similarity search - Component
Biological speciesBifidobacterium breve (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSuzuki, R. / Katayama, T. / Kim, B.-J. / Wakagi, T. / Shoun, H. / Ashida, H. / Yamamoto, K. / Fushinobu, S.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism
Authors: Suzuki, R. / Katayama, T. / Kim, B.-J. / Wakagi, T. / Shoun, H. / Ashida, H. / Yamamoto, K. / Fushinobu, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Overexpression, crystallization and preliminary X-ray analysis of xylulose-5-phosphate/fructose-6-phosphate phosphoketolase from Bifidobacterium breve
Authors: Suzuki, R. / Kim, B.-J. / Shibata, T. / Iwamoto, Y. / Katayama, T. / Ashida, H. / Wakagi, T. / Shoun, H. / Fushinobu, S. / Yamamoto, K.
History
DepositionApr 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,53316
Polymers94,9631
Non-polymers1,57015
Water15,961886
1
A: Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase
hetero molecules

A: Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,06532
Polymers189,9262
Non-polymers3,14030
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10580 Å2
ΔGint-35 kcal/mol
Surface area46560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.766, 174.766, 163.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-828-

NA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase / phosphoketolase


Mass: 94962.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium breve (bacteria) / Strain: 203 / Gene: xfp / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL
References: UniProt: D6PAH1, fructose-6-phosphate phosphoketolase

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Non-polymers , 6 types, 901 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 24%(v/v) PEG 6000, 0.1M BICINE buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2009 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 137590 / Num. obs: 137538 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 49.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 7.4 / Num. unique all: 6810 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→34.18 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.378 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18059 6904 5 %RANDOM
Rwork0.14995 ---
obs0.15148 130627 99.95 %-
all-137538 --
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: 19.729 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.074 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 100 886 7365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0226647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7221.9468997
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4424.551334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.538151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0991533
X-RAY DIFFRACTIONr_chiral_restr0.2410.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215160
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4541.53993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13126432
X-RAY DIFFRACTIONr_scbond_it3.44232654
X-RAY DIFFRACTIONr_scangle_it5.1894.52565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 515 -
Rwork0.179 9534 -
obs--99.66 %

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