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- PDB-6b15: Crystal structure of CBMbc (family CBM26) from Eubacterium rectal... -

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Basic information

Entry
Database: PDB / ID: 6b15
TitleCrystal structure of CBMbc (family CBM26) from Eubacterium rectale Amy13K
ComponentsAmy13K
KeywordsSUGAR BINDING PROTEIN / Carbohydrate Binding Module / Amylase / Starch / Gut Microbiome / Eubacterium rectale
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process / membrane
Similarity search - Function
Starch-binding module 26 / Starch-binding module 26 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesEubacterium rectale DSM 17629 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCockburn, D.W. / Wawrzak, Z. / Perez Medina, K. / Koropatkin, N.M.
CitationJournal: Mol. Microbiol. / Year: 2018
Title: Novel carbohydrate binding modules in the surface anchored alpha-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut.
Authors: Cockburn, D.W. / Suh, C. / Medina, K.P. / Duvall, R.M. / Wawrzak, Z. / Henrissat, B. / Koropatkin, N.M.
History
DepositionSep 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amy13K
B: Amy13K
C: Amy13K
D: Amy13K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0027
Polymers91,8164
Non-polymers1863
Water13,151730
1
A: Amy13K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0162
Polymers22,9541
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amy13K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0783
Polymers22,9541
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amy13K


Theoretical massNumber of molelcules
Total (without water)22,9541
Polymers22,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amy13K


Theoretical massNumber of molelcules
Total (without water)22,9541
Polymers22,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.730, 131.730, 151.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

21A-702-

HOH

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Components

#1: Protein
Amy13K


Mass: 22953.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale DSM 17629 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: D6DYI9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 4.14 Å3/Da / Density % sol: 70.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% Tacsimate, 0.1 M Bis-Tris Propane, pH 7.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→36.02 Å / Num. obs: 86483 / % possible obs: 98.46 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09175 / Rpim(I) all: 0.03852 / Net I/σ(I): 7.86
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.5615 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 8664 / CC1/2: 0.832 / Rpim(I) all: 0.237 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.1.2data reduction
Aimless0.5.8data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→36.02 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2288 1992 2.3 %
Rwork0.2004 --
obs0.2011 86456 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6393 0 12 731 7136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026567
X-RAY DIFFRACTIONf_angle_d0.738968
X-RAY DIFFRACTIONf_dihedral_angle_d12.3712204
X-RAY DIFFRACTIONf_chiral_restr0.029980
X-RAY DIFFRACTIONf_plane_restr0.0021140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.31811410.27646037X-RAY DIFFRACTION99
2.1525-2.21070.2981410.26496067X-RAY DIFFRACTION99
2.2107-2.27580.28751480.26496056X-RAY DIFFRACTION99
2.2758-2.34920.2741410.25156052X-RAY DIFFRACTION99
2.3492-2.43320.26551420.25046060X-RAY DIFFRACTION99
2.4332-2.53060.30721430.24826019X-RAY DIFFRACTION99
2.5306-2.64580.30521470.25516042X-RAY DIFFRACTION99
2.6458-2.78530.29661420.24466030X-RAY DIFFRACTION99
2.7853-2.95970.2851400.23956012X-RAY DIFFRACTION99
2.9597-3.18820.25631400.22426054X-RAY DIFFRACTION98
3.1882-3.5090.23391410.20315990X-RAY DIFFRACTION98
3.509-4.01650.20451420.17376029X-RAY DIFFRACTION98
4.0165-5.05930.16761410.14016016X-RAY DIFFRACTION97
5.0593-46.28340.15271430.15496000X-RAY DIFFRACTION95

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