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- PDB-6jhf: Crystal structure of apo Pullulanase from Paenibacillus barengoltzii -

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Basic information

Entry
Database: PDB / ID: 6jhf
TitleCrystal structure of apo Pullulanase from Paenibacillus barengoltzii
ComponentsPulullanase
KeywordsHYDROLASE / GH13 / Pullulanase
Function / homology
Function and homology information


pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Pullulanase, all-beta domain / Pullulanase, type I / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set ...: / Pullulanase, all-beta domain / Pullulanase, type I / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus barengoltzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsWu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii.
Authors: Huang, P. / Wu, S. / Yang, S. / Yan, Q. / Jiang, Z.
History
DepositionFeb 18, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 6, 2019ID: 5WVQ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pulullanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4175
Polymers75,1841
Non-polymers2334
Water16,736929
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.395, 98.583, 142.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Pulullanase


Mass: 75183.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-2 (ML) and 638-657 (GASGEAAAAAPAAAGGPPAG) had low-level electron density and were not included in the model.
Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Strain: CAU904 / Plasmid: pET-28a(+)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0C5GWS2, pullulanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08M calcium chloride, 0.1M MES, 22% PEG 3350, 0.7% beta-OG, pH 6.5
Temp details: 291-295

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 90-100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.708→50 Å / Num. obs: 76828 / % possible obs: 99 % / Redundancy: 12 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 25.2
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E8Y

2e8y


Resolution: 1.71→49.29 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.95
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.182 3785 4.93 %
Rwork0.152 --
obs0.153 76786 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5177 0 11 929 6117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065486
X-RAY DIFFRACTIONf_angle_d0.817486
X-RAY DIFFRACTIONf_dihedral_angle_d5.3125629
X-RAY DIFFRACTIONf_chiral_restr0.056800
X-RAY DIFFRACTIONf_plane_restr0.005991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7082-1.72980.22571290.17942449X-RAY DIFFRACTION91
1.7298-1.75260.25541140.18042625X-RAY DIFFRACTION97
1.7526-1.77660.24061230.17382592X-RAY DIFFRACTION97
1.7766-1.80190.19511650.16812619X-RAY DIFFRACTION97
1.8019-1.82880.21951270.16892626X-RAY DIFFRACTION99
1.8288-1.85740.1831230.16572719X-RAY DIFFRACTION99
1.8574-1.88790.20881260.16462671X-RAY DIFFRACTION99
1.8879-1.92040.22921430.19082692X-RAY DIFFRACTION99
1.9204-1.95540.2011510.17512666X-RAY DIFFRACTION100
1.9554-1.9930.2121410.1572675X-RAY DIFFRACTION100
1.993-2.03360.18181630.15042716X-RAY DIFFRACTION100
2.0336-2.07790.1681370.14632702X-RAY DIFFRACTION100
2.0779-2.12620.17241420.14892707X-RAY DIFFRACTION100
2.1262-2.17940.17441470.15052692X-RAY DIFFRACTION100
2.1794-2.23830.18161470.16242682X-RAY DIFFRACTION99
2.2383-2.30420.21961520.16662716X-RAY DIFFRACTION99
2.3042-2.37850.19931330.14252690X-RAY DIFFRACTION100
2.3785-2.46350.17991330.14332756X-RAY DIFFRACTION100
2.4635-2.56220.18221420.14742725X-RAY DIFFRACTION100
2.5622-2.67880.18621460.15162730X-RAY DIFFRACTION100
2.6788-2.820.16911340.15692753X-RAY DIFFRACTION100
2.82-2.99670.19461340.15592753X-RAY DIFFRACTION100
2.9967-3.2280.18651330.15882758X-RAY DIFFRACTION100
3.228-3.55270.17341510.14462752X-RAY DIFFRACTION100
3.5527-4.06660.16441470.13062771X-RAY DIFFRACTION99
4.0666-5.12270.14351540.12082818X-RAY DIFFRACTION100
5.1227-49.3120.1521480.15852946X-RAY DIFFRACTION99

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