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- PDB-7c8h: Ambient temperature structure of Bifidobacterium longum phosphoke... -

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Basic information

Entry
Database: PDB / ID: 7c8h
TitleAmbient temperature structure of Bifidobacterium longum phosphoketolase with thiamine diphosphate
ComponentsXylulose-5-phosphate/fructose-6-phosphate phosphoketolase
KeywordsLYASE / XFEL-SFX / ambient temperature / aldehyde-lyase activity / carbohydrate metabolic process / thiamine-diphosphate (ThDpp)
Function / homology
Function and homology information


fructose-6-phosphate phosphoketolase / fructose-6-phosphate phosphoketolase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
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. ...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. / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / MALONIC ACID / SUCCINIC ACID / THIAMINE DIPHOSPHATE / Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNakata, K. / Kashiwagi, T. / Nango, E. / Miyano, H. / Mizukoshi, T. / Iwata, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25650026 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)X-ray Free Electron Laser Priority Strategy Program Japan
Japan Society for the Promotion of Science (JSPS)19H05781 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X-ray crystallography.
Authors: Nakata, K. / Kashiwagi, T. / Kunishima, N. / Naitow, H. / Matsuura, Y. / Miyano, H. / Mizukoshi, T. / Tono, K. / Yabashi, M. / Nango, E. / Iwata, S.
History
DepositionJun 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
C: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
D: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
E: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
F: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
G: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
H: Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)752,25832
Polymers747,6008
Non-polymers4,65824
Water19,9251106
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.620, 185.800, 162.890
Angle α, β, γ (deg.)90.000, 99.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 93450.016 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: xfp / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6R2Q7, fructose-6-phosphate phosphoketolase

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Non-polymers , 6 types, 1130 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1106 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsDatabase reference is Q6R2Q7 which had been referred by PDB code 3AI7 according to author's request. ...Database reference is Q6R2Q7 which had been referred by PDB code 3AI7 according to author's request. Residue 575 is originally UNK.

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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: 2.89 Å3/Da / Density % sol: 57.38 % / Description: rod-like crystal
Crystal growTemperature: 298 K / Method: batch mode
Details: Equal amount of 15 mg ml-1 PKT solution (4 mM DTT, 10 mg ml-1 ThDpp) and precipitant solution (50 mM malonate, 12% tacsimate (pH5), 17% PEG3350) were mixed in order to prepare seed crystals. ...Details: Equal amount of 15 mg ml-1 PKT solution (4 mM DTT, 10 mg ml-1 ThDpp) and precipitant solution (50 mM malonate, 12% tacsimate (pH5), 17% PEG3350) were mixed in order to prepare seed crystals. Preparations of seed crystals of PKT were performed by utilizing light induced crystallization method which promoted to form initial crystal nucleus by evanescent field arised from light irradiation to gold nano-particle vapored on general polystyrene plate (Fujifilm Wako). After 16 h, precipitated crystals were homogenized and centrifuged to use supernatant as seed solution. For the purpose of forming micro-sized crystals of PKT, 1176 micro l of protein-precipitant solution mixture as the same components of seed crystals preparation was mixed with 120 micro l of the seed solution in a 1.5 ml tube. After gentle rotation at 25 degree C for 2 h, the supernatant was exchanged to the same precipitant solution. The same buffer exchange was iteratively conducted after 10 h and 16 h.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7714 Å
DetectorType: MPCCD / Detector: CCD / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7714 Å / Relative weight: 1
ReflectionResolution: 2.5→46.8 Å / Num. obs: 292114 / % possible obs: 100 % / Redundancy: 234 % / Biso Wilson estimate: 57.854 Å2 / CC1/2: 0.938 / R split: 0.215 / Net I/σ(I): 3.64
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 165.2 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 29113 / CC1/2: 0.493 / R split: 1.006 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Cheetahdata collection
CrystFEL0.6.1data processing
MOLREP11.0.05phasing
Coot0.8.9model building
CrystFEL0.6.1data reduction
CrystFEL0.6.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AI7

3ai7


Resolution: 2.5→46.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.1757 / FOM work R set: 0.7736 / SU B: 11.561 / SU ML: 0.236 / SU R Cruickshank DPI: 0.3659 / SU Rfree: 0.2414 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 14633 5 %RANDOM
Rwork0.1613 ---
obs0.1642 277500 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.71 Å2 / Biso mean: 54.255 Å2 / Biso min: 25.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-0.48 Å2
2---1 Å20 Å2
3---1.94 Å2
Refinement stepCycle: final / Resolution: 2.5→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51353 0 279 1106 52738
Biso mean--51.99 46.53 -
Num. residues----6457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01353092
X-RAY DIFFRACTIONr_bond_other_d0.0010.01746814
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.64172236
X-RAY DIFFRACTIONr_angle_other_deg1.2771.575108827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5656459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2523.0762975
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.076158383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6515264
X-RAY DIFFRACTIONr_chiral_restr0.0670.26711
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0260371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211337
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 1109 -
Rwork0.37 20416 -
all-21525 -
obs--99.94 %

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