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- PDB-8xi1: Cellodextrin phosphorylase from Clostridium thermocellum mutant -... -

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Basic information

Entry
Database: PDB / ID: 8xi1
TitleCellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines
Componentscellodextrin phosphorylase variant
KeywordsCARBOHYDRATE / Cellulose / Cellodextrin / Synthesis / Phosphorolysis
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsKuga, T. / Sunagawa, N. / Igarashi, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12566 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H05494 Japan
CitationJournal: To Be Published
Title: Effect of free cysteine residues to serine mutation on cellodextrin phosphorylase
Authors: Kuga, T. / Sunagawa, N. / Igarashi, K.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 25, 2024ID: 8H2K
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cellodextrin phosphorylase variant
B: cellodextrin phosphorylase variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,15214
Polymers225,3582
Non-polymers79312
Water45,5242527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-81 kcal/mol
Surface area69130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.441, 89.048, 88.989
Angle α, β, γ (deg.)98.884, 110.547, 110.674
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cellodextrin phosphorylase variant


Mass: 112679.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Strain: YM4 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 2539 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2527 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10 mg/ml protein solution was mixed 1:1 with an optimized solution consisting of 100 mM pH 5.0 sodium acetate, 12% PEG4000, and 5% glycerol with streak seeding

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→43.76 Å / Num. obs: 418204 / % possible obs: 93.49 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.99
Reflection shellResolution: 1.37→1.419 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 41686 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
PHENIXphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→43.76 Å / SU ML: 0.1835 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.3928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2001 21009 5.02 %
Rwork0.1743 397158 -
obs0.1756 418168 93.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.39 Å2
Refinement stepCycle: LAST / Resolution: 1.37→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15746 0 47 2527 18320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008316700
X-RAY DIFFRACTIONf_angle_d0.957722662
X-RAY DIFFRACTIONf_chiral_restr0.0782458
X-RAY DIFFRACTIONf_plane_restr0.00892969
X-RAY DIFFRACTIONf_dihedral_angle_d14.30196185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.3777080.36913132X-RAY DIFFRACTION93.15
1.39-1.40.36286970.343113223X-RAY DIFFRACTION93.24
1.4-1.420.31927210.318713192X-RAY DIFFRACTION93.39
1.42-1.440.32336580.301313274X-RAY DIFFRACTION93.64
1.44-1.460.27766270.264813313X-RAY DIFFRACTION93.64
1.46-1.480.27276970.244313280X-RAY DIFFRACTION93.84
1.48-1.50.27146870.241613349X-RAY DIFFRACTION93.98
1.5-1.520.25517000.220413287X-RAY DIFFRACTION94.06
1.52-1.540.24136540.221913453X-RAY DIFFRACTION94.23
1.54-1.570.25516090.225213452X-RAY DIFFRACTION94.39
1.57-1.60.2376960.221713394X-RAY DIFFRACTION94.53
1.6-1.620.22447370.203413263X-RAY DIFFRACTION93.91
1.62-1.660.24387510.20113236X-RAY DIFFRACTION93.8
1.66-1.690.2297100.196713419X-RAY DIFFRACTION94.58
1.69-1.730.22456790.189113453X-RAY DIFFRACTION94.74
1.73-1.770.21097270.189913304X-RAY DIFFRACTION94.53
1.77-1.810.22417900.183913373X-RAY DIFFRACTION94.35
1.81-1.860.2087050.187713304X-RAY DIFFRACTION94.14
1.86-1.910.23147400.212713124X-RAY DIFFRACTION93.11
1.91-1.980.25377000.222313074X-RAY DIFFRACTION92.16
1.98-2.050.17897400.169113139X-RAY DIFFRACTION93.28
2.05-2.130.18586490.162813299X-RAY DIFFRACTION93.14
2.13-2.230.18836870.166913090X-RAY DIFFRACTION92.54
2.23-2.340.24336690.18812379X-RAY DIFFRACTION87.42
2.34-2.490.1886790.15113142X-RAY DIFFRACTION92.9
2.49-2.680.20016720.151113191X-RAY DIFFRACTION92.97
2.68-2.950.18677370.153413137X-RAY DIFFRACTION92.99
2.95-3.380.17257490.143413232X-RAY DIFFRACTION93.85
3.38-4.260.14787530.132813293X-RAY DIFFRACTION94.1
4.26-43.760.16736810.151913357X-RAY DIFFRACTION94.13

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