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- PDB-2zyk: Crystal structure of cyclo/maltodextrin-binding protein complexed... -

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Basic information

Entry
Database: PDB / ID: 2zyk
TitleCrystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin
ComponentsSolute-binding protein
KeywordsSUGAR BINDING PROTEIN / solute-binding protein / closed form
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
gamma-cyclodextrin / Maltodextrin-binding protein
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTonozuka, T. / Sogawa, A. / Yamada, M. / Matsumoto, N. / Yoshida, H. / Kamitori, S. / Ichikawa, K. / Mizuno, M. / Nishikawa, A. / Sakano, Y.
Citation
Journal: Febs J. / Year: 2007
Title: Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein
Authors: Tonozuka, T. / Sogawa, A. / Yamada, M. / Matsumoto, N. / Yoshida, H. / Kamitori, S. / Ichikawa, K. / Mizuno, M. / Nishikawa, A. / Sakano, Y.
#1: Journal: Febs J. / Year: 2009
Title: Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein
Authors: Matsumoto, M. / Yamada, M. / Kurakata, Y. / Yoshida, H. / Kamitori, S. / Nishikawa, A. / Tonozuka, T.
History
DepositionJan 26, 2009Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 10, 2009ID: 2DFZ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 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_validate_close_contact / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute-binding protein
B: Solute-binding protein
C: Solute-binding protein
D: Solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,0088
Polymers174,7474
Non-polymers5,2614
Water9,692538
1
A: Solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0022
Polymers43,6871
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0022
Polymers43,6871
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0022
Polymers43,6871
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0022
Polymers43,6871
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.399, 95.270, 117.130
Angle α, β, γ (deg.)90.00, 131.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Solute-binding protein / Cyclodextrin-binding protein


Mass: 43686.863 Da / Num. of mol.: 4 / Fragment: residues 1-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Strain: R-47 / Plasmid: pETCBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJF5
#2: Polysaccharide
Cyclooctakis-(1-4)-(alpha-D-glucopyranose) / gamma-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1315.142 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: gamma-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,8,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a1-h4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1WURCSPDB2Glycan 1.1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 25% PEG 6000, 0.1M MES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 47691 / Num. obs: 47691 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24
Reflection shellResolution: 2.5→2.66 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 8.6 / Num. unique all: 4735 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: a rough model of the selenomethionine-substituted protein

Resolution: 2.5→48.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3030046.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 4881 10.2 %RANDOM
Rwork0.222 ---
obs0.222 47650 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0713 Å2 / ksol: 0.361716 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å22.22 Å2
2--4.19 Å20 Å2
3----1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11856 0 352 538 12746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 790 10.1 %
Rwork0.267 7039 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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