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- PDB-7znp: Structure of AmedSP -

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Basic information

Entry
Database: PDB / ID: 7znp
TitleStructure of AmedSP
ComponentsSucrose phosphorylase
KeywordsHYDROLASE / Enzyme / phosphorylase
Function / homology
Function and homology information


1,4-alpha-oligoglucan phosphorylase activity / carbohydrate metabolic process
Similarity search - Function
Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Sucrose phosphorylase
Similarity search - Component
Biological speciesAlteromonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFredslund, F. / Teze, D. / Welner, D.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20CC0035580 Denmark
CitationJournal: To Be Published
Title: Structure of AmedSP
Authors: Fredslund, F. / Teze, D. / Welner, D.H.
History
DepositionApr 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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

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Assembly

Deposited unit
A: Sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7203
Polymers55,6601
Non-polymers602
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.456, 143.558, 72.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Sucrose phosphorylase


Mass: 55659.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Gene: BM525_11180 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1J0SGS2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60 % v/v T-mate pH 7.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2021 / Details: CRL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.15→42.2 Å / Num. obs: 72691 / % possible obs: 99.64 % / Observed criterion σ(F): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 60.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1465 / Rpim(I) all: 0.04125 / Rrim(I) all: 0.1523 / Net I/σ(I): 11.14
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 11.8 % / Num. unique obs: 3658 / CC1/2: 0.313 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R7A

1r7a


Resolution: 2.15→42.2 Å / SU ML: 0.3295 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.6668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 2040 2.81 %
Rwork0.1854 70651 -
obs0.1866 72691 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.26 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 2 107 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393979
X-RAY DIFFRACTIONf_angle_d0.61445413
X-RAY DIFFRACTIONf_chiral_restr0.0437613
X-RAY DIFFRACTIONf_plane_restr0.0045710
X-RAY DIFFRACTIONf_dihedral_angle_d12.21631415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.35761310.36524515X-RAY DIFFRACTION95.79
2.2-2.260.33791390.34974755X-RAY DIFFRACTION99.57
2.26-2.320.35381340.36474687X-RAY DIFFRACTION99.94
2.32-2.380.3591350.31464704X-RAY DIFFRACTION100
2.38-2.460.30071360.2794733X-RAY DIFFRACTION100
2.46-2.550.27441360.24364744X-RAY DIFFRACTION99.94
2.55-2.650.28441390.23414748X-RAY DIFFRACTION100
2.65-2.770.2681320.24054724X-RAY DIFFRACTION99.98
2.77-2.920.26991330.22214707X-RAY DIFFRACTION99.98
2.92-3.10.31191380.20454715X-RAY DIFFRACTION99.96
3.1-3.340.22071380.19094737X-RAY DIFFRACTION99.94
3.34-3.680.20281370.17984733X-RAY DIFFRACTION100
3.68-4.210.22891380.14664693X-RAY DIFFRACTION99.3
4.21-5.30.18911390.1474729X-RAY DIFFRACTION99.98
5.3-42.20.18561350.1554727X-RAY DIFFRACTION99.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.608939741920.3524928964460.4246993966661.559860857610.1920765777230.871727874521-0.0180718450838-0.1373425464160.2706045048080.0171436871425-0.06799206047810.175000793404-0.251639106382-0.1264258370434.86924510156E-50.6063366570210.101460435955-0.03565479806550.555532943292-0.07139424097070.68075767838717.39023841770.498427758220.489282715
21.63775002670.357118395679-1.435551968171.86889903477-0.5867568207472.86084841241-0.05515193505950.0281168110803-0.000247988170185-0.0937802820388-0.0859816717057-0.192731450649-0.2156121276640.479983876149-0.000192773530150.630609197968-0.0310461484885-0.09367307983690.762151951804-0.04151632955120.61327778131442.890956925173.000093518612.4763632277
31.003343488030.3093712806310.004897978050780.746428546554-0.1025793044980.8613007801970.0868412236142-0.149689428889-0.09817244775280.0677227349973-0.090600475762-0.1116727523990.02715667602650.221622583643-6.87396577414E-50.5667819359010.0850726950141-0.06659659216540.621088710921-0.03564782211510.5714955736831.045143162953.299229481721.0958637763
40.244270283503-0.1302652224270.2666695858810.448418073581-0.3115927681860.3501144945550.1306518026980.500733964877-0.000717291660032-0.495960138308-0.312770595957-0.2421463896140.3026912201750.2674237808784.82484423366E-50.7328639777150.120333707333-0.01444365619470.644613288157-0.0480937817940.66471582900423.783766067843.91252281373.55752740178
51.19053214970.525685685332-0.3193988120432.21004590362-1.012738216792.532526090020.0222652635157-0.0781289325724-0.08256078221170.0386354631943-0.05491848182840.2058682888890.186166466763-0.09175359323529.97596125323E-50.5498156825380.0467774848249-0.008550886621990.56745863805-0.0556927596610.6203549212839.797560246549.108272521120.4296123129
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 79 )3 - 791 - 77
22chain 'A' and (resid 80 through 195 )80 - 19578 - 193
33chain 'A' and (resid 196 through 308 )196 - 308194 - 306
44chain 'A' and (resid 309 through 350 )309 - 350307 - 348
55chain 'A' and (resid 351 through 504 )351 - 504349 - 502

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