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- PDB-3k8k: Crystal structure of SusG -

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Basic information

Entry
Database: PDB / ID: 3k8k
TitleCrystal structure of SusG
ComponentsAlpha-amylase, susG
KeywordsMEMBRANE PROTEIN / amylase / alpha8/beta8 barrel / CBM / beta-sandwich
Function / homology
Function and homology information


starch catabolic process / oligosaccharide catabolic process / starch binding / alpha-amylase / outer membrane / alpha-amylase activity / cell outer membrane / calcium ion binding / magnesium ion binding
Similarity search - Function
: / Carbohydrate binding domain (family 58) / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...: / Carbohydrate binding domain (family 58) / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Alpha-amylase SusG
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.2 Å
AuthorsKoropatkin, N.M. / Smith, T.J.
CitationJournal: Structure / Year: 2010
Title: SusG: A Unique Cell-Membrane-Associated alpha-Amylase from a Prominent Human Gut Symbiont Targets Complex Starch Molecules.
Authors: Koropatkin, N.M. / Smith, T.J.
History
DepositionOct 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase, susG
B: Alpha-amylase, susG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,99225
Polymers151,6552
Non-polymers1,33723
Water8,359464
1
A: Alpha-amylase, susG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,79317
Polymers75,8281
Non-polymers96516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-amylase, susG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1998
Polymers75,8281
Non-polymers3727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.038, 128.038, 129.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-amylase, susG /


Mass: 75827.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_3698, SusG / Plasmid: pET-28rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8A1G3

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Non-polymers , 6 types, 487 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11mg/ml protein, 100mM HEPES, 200mM Magnesium Acetate, 18% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 30, 2008 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→500 Å / Num. obs: 94667 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.065 / Net I/σ(I): 28.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 4119 / Rsym value: 0.224

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.843 / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.23 9435 8.9 %
Rwork0.196 --
obs-94532 89.2 %
Solvent computationBsol: 31.479 Å2
Displacement parametersBiso max: 93.97 Å2 / Biso mean: 42.625 Å2 / Biso min: 18.78 Å2
Baniso -1Baniso -2Baniso -3
1-10.27 Å20 Å20 Å2
2--10.27 Å20 Å2
3----20.54 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10347 0 83 464 10894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.217
X-RAY DIFFRACTIONc_mcbond_it1.2251.5
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_mcangle_it1.8952
X-RAY DIFFRACTIONc_scangle_it3.0042.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5eg.parameg.top

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