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- PDB-1r7a: Sucrose Phosphorylase from Bifidobacterium adolescentis -

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Basic information

Entry
Database: PDB / ID: 1r7a
TitleSucrose Phosphorylase from Bifidobacterium adolescentis
Componentssucrose phosphorylase
KeywordsTRANSFERASE / beta-alpha-barrels / dimer / glycoside hydrolase
Function / homology
Function and homology information


sucrose phosphorylase / sucrose phosphorylase activity / carbohydrate metabolic process
Similarity search - Function
alpha-Amylases / Sucrose phosphorylase, C-terminal / Sucrose phosphorylase, C-terminal / Glycosyl hydrolase fold / Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain ...alpha-Amylases / Sucrose phosphorylase, C-terminal / Sucrose phosphorylase, C-terminal / Glycosyl hydrolase fold / Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Single Sheet / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sucrose phosphorylase / Sucrose phosphorylase
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.77 Å
AuthorsSprogoe, D. / van den Broek, L.A.M. / Mirza, O. / Kastrup, J.S. / Voragen, A.G.J. / Gajhede, M. / Skov, L.K.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.
Authors: Sprogoe, D. / van den Broek, L.A. / Mirza, O. / Kastrup, J.S. / Voragen, A.G. / Gajhede, M. / Skov, L.K.
History
DepositionOct 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 19, 2014Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sucrose phosphorylase
B: sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8144
Polymers112,5692
Non-polymers2442
Water25,5991421
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.040, 123.360, 151.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is probably a dimer (chains A and B) as given in the coordinates.

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Components

#1: Protein sucrose phosphorylase


Mass: 56284.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (bacteria)
Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue MRF
References: UniProt: Q84HQ2, UniProt: A0ZZH6*PLUS, sucrose phosphorylase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1421 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, sodium acetate, tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5-1.0 mg/mlprotein1drop
210 mMTris-HCl1droppH7.1
327 %(w/v)PEG40001reservoir
40.1 MTris-HCl1reservoirpH8.5
50.1 Msodium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21201
31201
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.542
SYNCHROTRONMAX_II I711MAX II BEAMLINE I71120.996
SYNCHROTRONBESSY 14.230.918
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMay 11, 2003
MARRESEARCH2CCDJun 20, 2003
MARRESEARCH3CCDJun 26, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1osmic mirrorSINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
3Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.5421
20.9961
30.9181
ReflectionResolution: 1.58→23.3 Å / Num. all: 138899 / Num. obs: 138899 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.109 / Net I/σ(I): 4.3
Reflection shellResolution: 1.58→1.66 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.9 / Num. unique all: 17475 / Rsym value: 0.53 / % possible all: 97.8
Reflection
*PLUS
Rmerge(I) obs: 0.109
Reflection shell
*PLUS
% possible obs: 85.2 % / Rmerge(I) obs: 0.53

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.77→19.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2663906.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 5198 5.1 %RANDOM
Rwork0.164 ---
all0.164 101172 --
obs0.164 101172 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.2152 Å2 / ksol: 0.379705 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.77→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7934 0 16 1421 9371
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 1.77→1.88 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.213 858 5.2 %
Rwork0.192 15777 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3LG_CNS.PARLG_CNS.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 101196 / % reflection Rfree: 5 % / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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