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- PDB-3ck8: B. thetaiotaomicron SusD with beta-cyclodextrin -

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Basic information

Entry
Database: PDB / ID: 3ck8
TitleB. thetaiotaomicron SusD with beta-cyclodextrin
ComponentsSusD
KeywordsSUGAR BINDING PROTEIN / TPR repeat / carbohydrate binding / starch binding
Function / homology
Function and homology information


starch metabolic process / starch catabolic process / starch binding / outer membrane / cell outer membrane / calcium ion binding / identical protein binding
Similarity search - Function
TPR-like / SusD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / RagB/SusD domain / SusD family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily ...TPR-like / SusD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / RagB/SusD domain / SusD family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
beta-cyclodextrin / Starch-binding protein SusD
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKoropatkin, N.M. / Martens, E.C. / Gordon, J.I. / Smith, T.J.
CitationJournal: Structure / Year: 2008
Title: Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.
Authors: Koropatkin, N.M. / Martens, E.C. / Gordon, J.I. / Smith, T.J.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / 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_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusD
B: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,65418
Polymers119,5672
Non-polymers3,08716
Water17,799988
1
A: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,38910
Polymers59,7831
Non-polymers1,6069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2658
Polymers59,7831
Non-polymers1,4817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.670, 73.140, 83.550
Angle α, β, γ (deg.)65.060, 71.950, 69.760
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SusD


Mass: 59783.340 Da / Num. of mol.: 2 / Fragment: UNP residues 26-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: SusD / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8A1G2
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ORIGINAL SUSD GENE SEQUENCE DEPOSITED BY WASHINGTON UNIVERSITY (FROM JEFFREY I GORDON'S ...THE ORIGINAL SUSD GENE SEQUENCE DEPOSITED BY WASHINGTON UNIVERSITY (FROM JEFFREY I GORDON'S LABORATORY) IS INCORRECT. THE SAME LAB HAS SUBSEQUENTLY RE-SEQUENCED THE GENE AND CONFIRMED THAT LYS IS THE CORRECT AMINO ACID AT THIS POSITION.

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: seeding in batch / pH: 6
Details: 50mM sodium cacodylate, 75mM Calcium acetate, 14% PEG 8000, 10mM beta-cyclodextrin, pH 6.0, seeding in batch, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Sep 1, 2007 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→60.2 Å / Num. all: 66380 / Num. obs: 66380 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.033 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 8307 / Rsym value: 0.073 / % possible all: 82.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CK9

3ck9


Resolution: 2.1→60.19 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 6638 9.6 %random
Rwork0.169 ---
all0.169 65461 --
obs0.169 65461 95.1 %-
Solvent computationBsol: 43.241 Å2
Displacement parametersBiso mean: 16.416 Å2
Baniso -1Baniso -2Baniso -3
1--3.515 Å25.154 Å2-3.318 Å2
2--0.567 Å20.171 Å2
3---2.948 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8049 0 198 988 9235
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.178
X-RAY DIFFRACTIONc_mcbond_it1.0671.5
X-RAY DIFFRACTIONc_scbond_it1.8632
X-RAY DIFFRACTIONc_mcangle_it1.532
X-RAY DIFFRACTIONc_scangle_it2.5312.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5bcd2.parambcd2.top

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