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- PDB-6b3p: Crystal structure of CBMbc (family CBM26) from Eubacterium rectal... -

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Basic information

Entry
Database: PDB / ID: 6b3p
TitleCrystal structure of CBMbc (family CBM26) from Eubacterium rectale Amy13K in Complex with Maltoheptaose
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 / membrane => GO:0016020 / carbohydrate metabolic process
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
alpha-maltotriose / alpha-maltotetraose / FORMIC ACID / Glycosidases
Similarity search - Component
Biological speciesEubacterium rectale DSM 17629 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsCockburn, D.W. / Wawrzak, Z. / Perez Medina, K. / Koropatkin, N.M.
Funding support United States, 3items
OrganizationGrant numberCountry
University of Michigan Gastrointestinal Peptides Research CenterDK034933 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor085P1000817 United States
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 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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 1.3Dec 4, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Feb 19, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / computing / entity / pdbx_nonpoly_scheme / refine / reflns / struct_conn / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _chem_comp.type ..._atom_site.label_alt_id / _chem_comp.type / _computing.structure_refinement / _entity.src_method / _pdbx_nonpoly_scheme.auth_seq_num / _refine.ls_R_factor_R_work / _refine.ls_percent_reflns_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.percent_possible_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amy13K
B: Amy13K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,11741
Polymers45,9082
Non-polymers4,21039
Water9,944552
1
A: Amy13K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,03620
Polymers22,9541
Non-polymers2,08219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint47 kcal/mol
Surface area13370 Å2
MethodPISA
2
B: Amy13K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,08221
Polymers22,9541
Non-polymers2,12820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint11 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.200, 134.200, 231.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-745-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Amy13K


Mass: 22953.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale DSM 17629 (bacteria)
Gene: ERE_20420 / Production host: Escherichia coli (E. coli) / References: UniProt: D4JJZ5

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 587 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 6.54 Å3/Da / Density % sol: 81.2 %
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: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.01→28.15 Å / Num. obs: 81845 / % possible obs: 99.7 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.1781 / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.1.2data reduction
Aimless0.5.8data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B15

6b15


Resolution: 2.01→28.15 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.39
RfactorNum. reflection% reflection
Rfree0.196 1998 2.44 %
Rwork0.184 --
obs0.184 81782 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.01→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 279 552 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053590
X-RAY DIFFRACTIONf_angle_d0.9334840
X-RAY DIFFRACTIONf_dihedral_angle_d12.0851245
X-RAY DIFFRACTIONf_chiral_restr0.392554
X-RAY DIFFRACTIONf_plane_restr0.002581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.06030.30381370.29775571X-RAY DIFFRACTION99
2.0603-2.11590.30331410.2745579X-RAY DIFFRACTION99
2.1159-2.17820.27651390.27075601X-RAY DIFFRACTION99
2.1782-2.24850.25091410.24515601X-RAY DIFFRACTION100
2.2485-2.32880.26381420.24185636X-RAY DIFFRACTION100
2.3288-2.4220.23821410.22315622X-RAY DIFFRACTION100
2.422-2.53210.23791420.21995665X-RAY DIFFRACTION100
2.5321-2.66550.23231400.21245649X-RAY DIFFRACTION100
2.6655-2.83240.22291430.20315670X-RAY DIFFRACTION100
2.8324-3.05090.1971430.19765718X-RAY DIFFRACTION100
3.0509-3.35740.18071440.1715735X-RAY DIFFRACTION100
3.3574-3.84220.14651440.15175774X-RAY DIFFRACTION100
3.8422-4.83680.15281470.12965847X-RAY DIFFRACTION100
4.8368-28.1810.16911540.15456116X-RAY DIFFRACTION100

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