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- PDB-5ynh: Crystal structure of Pullulanase from Klebsiella pneumoniae compl... -

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Basic information

Entry
Database: PDB / ID: 5ynh
TitleCrystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin
ComponentsPulA protein
KeywordsHYDROLASE / alpha-amylase / pullulanase / Klebsiella pneumoniae / crystal / gamma-cyclodextrin / co-crystallization
Function / homology
Function and homology information


pullulanase / pullulanase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Pullulanase, Ins domain / Pullulanase Ins domain / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain ...Pullulanase, Ins domain / Pullulanase Ins domain / Pullulanase, carbohydrate-binding module 41 / Bacterial pullanase-associated domain / Alpha-1,6-glucosidases, pullulanase-type / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase, N2 domain / Alpha-1,6-glucosidases, pullulanase-type, C-terminal / Pullulanase N2 domain / Rab geranylgeranyltransferase alpha-subunit, insert domain / Immunoglobulin-like - #1110 / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Carbohydrate-binding-like fold / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
gamma-cyclodextrin / pullulanase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSaka, N. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04909 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin
Authors: Saka, N. / Iwamoto, H. / Malle, D. / Takahashi, N. / Mizutani, K. / Mikami, B.
History
DepositionOct 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._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_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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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: PulA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2429
Polymers119,3191
Non-polymers2,9238
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area37300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.206, 89.206, 298.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PulA protein / Pullulanase


Mass: 119318.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella pneumoniae (bacteria) / References: UniProt: W9BQ28
#2: Polysaccharide Cyclooctakis-(1-4)-(alpha-D-glucopyranose) / gamma-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1315.142 Da / Num. of mol.: 2
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M magnesium sulfate, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 76149 / % possible obs: 99.03 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09923 / Net I/σ(I): 19.04
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.4279 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 7539 / CC1/2: 0.936 / % possible all: 99.31

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FGZ

2fgz


Resolution: 2.05→49.67 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.36
RfactorNum. reflection% reflection
Rfree0.2578 3878 5.09 %
Rwork0.205 --
obs0.2077 76130 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 187 349 8611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078485
X-RAY DIFFRACTIONf_angle_d0.89911591
X-RAY DIFFRACTIONf_dihedral_angle_d15.8725067
X-RAY DIFFRACTIONf_chiral_restr0.0531349
X-RAY DIFFRACTIONf_plane_restr0.0061493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.07510.37251330.27642550X-RAY DIFFRACTION99
2.0751-2.10130.31471330.2752552X-RAY DIFFRACTION100
2.1013-2.1290.36631430.2662527X-RAY DIFFRACTION99
2.129-2.15820.33711480.262521X-RAY DIFFRACTION100
2.1582-2.1890.32751550.25472527X-RAY DIFFRACTION99
2.189-2.22170.33461510.24542542X-RAY DIFFRACTION99
2.2217-2.25640.29371340.24932544X-RAY DIFFRACTION99
2.2564-2.29340.32861390.24132562X-RAY DIFFRACTION99
2.2934-2.33290.32121500.2392532X-RAY DIFFRACTION100
2.3329-2.37530.31081370.23992532X-RAY DIFFRACTION99
2.3753-2.4210.29011170.23392565X-RAY DIFFRACTION99
2.421-2.47040.29881350.23472555X-RAY DIFFRACTION99
2.4704-2.52410.32261430.24762562X-RAY DIFFRACTION99
2.5241-2.58290.3131090.24482569X-RAY DIFFRACTION99
2.5829-2.64750.32311430.23932520X-RAY DIFFRACTION98
2.6475-2.7190.32491350.23942552X-RAY DIFFRACTION98
2.719-2.7990.30891180.23312576X-RAY DIFFRACTION98
2.799-2.88940.27981300.23652564X-RAY DIFFRACTION98
2.8894-2.99260.28491450.22642535X-RAY DIFFRACTION98
2.9926-3.11240.26931480.22212531X-RAY DIFFRACTION98
3.1124-3.25410.28311650.22562561X-RAY DIFFRACTION99
3.2541-3.42560.24521420.20992588X-RAY DIFFRACTION98
3.4256-3.64010.25381490.19242568X-RAY DIFFRACTION99
3.6401-3.92110.2021220.18032650X-RAY DIFFRACTION99
3.9211-4.31550.19021260.15982653X-RAY DIFFRACTION100
4.3155-4.93950.19071360.14332693X-RAY DIFFRACTION100
4.9395-6.22130.20241470.1662721X-RAY DIFFRACTION100
6.2213-49.68410.17161450.15482900X-RAY DIFFRACTION99

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