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- PDB-5yn2: Crystal structure of apo Pullulanase from Klebsiella pneumoniae i... -

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Basic information

Entry
Database: PDB / ID: 5yn2
TitleCrystal structure of apo Pullulanase from Klebsiella pneumoniae in space group P43212
ComponentsPulA protein
KeywordsHYDROLASE / alpha-amylase / pullulanase / Klebsiella pneumoniae / crystal
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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)119,5046
Polymers119,3191
Non-polymers1855
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.038, 89.038, 301.843
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M magnesium sulfate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.301→50 Å / Num. obs: 54725 / % possible obs: 99.27 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07093 / Net I/σ(I): 18.08
Reflection shellResolution: 2.301→2.383 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.75 / Num. unique obs: 5298 / CC1/2: 0.867 / % possible all: 98.22

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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: 2.301→43.799 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2423 2778 5.08 %
Rwork0.1844 --
obs0.1873 54661 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.301→43.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8067 0 5 416 8488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088262
X-RAY DIFFRACTIONf_angle_d0.87611260
X-RAY DIFFRACTIONf_dihedral_angle_d17.7234930
X-RAY DIFFRACTIONf_chiral_restr0.0521265
X-RAY DIFFRACTIONf_plane_restr0.0051483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3012-2.34080.28551270.23292512X-RAY DIFFRACTION97
2.3408-2.38340.28651280.23222531X-RAY DIFFRACTION99
2.3834-2.42920.31641550.22752527X-RAY DIFFRACTION99
2.4292-2.47880.27671340.23682549X-RAY DIFFRACTION99
2.4788-2.53270.31441430.23062521X-RAY DIFFRACTION99
2.5327-2.59160.29281260.22632539X-RAY DIFFRACTION99
2.5916-2.65640.28611450.22082578X-RAY DIFFRACTION99
2.6564-2.72820.26471400.21812551X-RAY DIFFRACTION99
2.7282-2.80850.25121440.21252555X-RAY DIFFRACTION99
2.8085-2.89910.32561400.21272554X-RAY DIFFRACTION99
2.8991-3.00270.27651260.21852597X-RAY DIFFRACTION100
3.0027-3.12290.28151350.21262579X-RAY DIFFRACTION100
3.1229-3.2650.29871460.21742593X-RAY DIFFRACTION100
3.265-3.43710.27281290.21142617X-RAY DIFFRACTION100
3.4371-3.65230.25291440.19122585X-RAY DIFFRACTION100
3.6523-3.93420.2511430.18132641X-RAY DIFFRACTION100
3.9342-4.32980.19761270.15532643X-RAY DIFFRACTION100
4.3298-4.95560.17991360.13962684X-RAY DIFFRACTION100
4.9556-6.24060.21781750.15752663X-RAY DIFFRACTION100
6.2406-43.80740.17481350.14722864X-RAY DIFFRACTION98

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