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- PDB-6jhg: Crystal structure of apo Pullulanase from Paenibacillus barengolt... -

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Basic information

Entry
Database: PDB / ID: 6jhg
TitleCrystal structure of apo Pullulanase from Paenibacillus barengoltzii in space group P212121
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: 1.891 Å
AuthorsWu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q.
CitationJournal: To Be Published
Title: Crystal structure of apo Pullulanase from Paenibacillus barengoltzii in space group P212121
Authors: Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q.
History
DepositionFeb 18, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 6, 2019ID: 5WWB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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)75,2593
Polymers75,1841
Non-polymers762
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.457, 78.834, 116.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 1-11 (MLSVQKEFHGT) and 638-657 (GASGEAAAAAPAAAGGPPAG) had low-level electron density and were not included in the model
Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Strain: CAU940 / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.02M HEPES pH 6.5, 21% PEG 3350, 0.7% beta-OG / 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: BSRF / Beamline: 3W1A / Wavelength: 0.97924 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.891→50 Å / Num. obs: 53244 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.551
Reflection shellResolution: 1.891→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 2669 / % possible all: 97.1

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Processing

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

2e8y


Resolution: 1.891→28.631 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2009 2587 4.86 %
Rwork0.1571 --
obs0.1591 53241 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.891→28.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5105 0 2 614 5721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075410
X-RAY DIFFRACTIONf_angle_d0.7937371
X-RAY DIFFRACTIONf_dihedral_angle_d6.034375
X-RAY DIFFRACTIONf_chiral_restr0.053777
X-RAY DIFFRACTIONf_plane_restr0.005985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8907-1.92710.30821250.24082501X-RAY DIFFRACTION88
1.9271-1.96640.2791440.21242780X-RAY DIFFRACTION100
1.9664-2.00910.26931510.1912811X-RAY DIFFRACTION100
2.0091-2.05590.20191370.17332798X-RAY DIFFRACTION100
2.0559-2.10730.22181500.16652827X-RAY DIFFRACTION100
2.1073-2.16420.23551420.16372808X-RAY DIFFRACTION100
2.1642-2.22790.20541490.15712808X-RAY DIFFRACTION100
2.2279-2.29980.22051570.16422795X-RAY DIFFRACTION100
2.2998-2.38190.20931330.15872843X-RAY DIFFRACTION100
2.3819-2.47720.20751710.1542802X-RAY DIFFRACTION100
2.4772-2.58990.22421330.15392858X-RAY DIFFRACTION100
2.5899-2.72630.16931410.1542823X-RAY DIFFRACTION100
2.7263-2.8970.19371550.15312853X-RAY DIFFRACTION100
2.897-3.12040.21371390.1682847X-RAY DIFFRACTION100
3.1204-3.4340.21221420.16422878X-RAY DIFFRACTION100
3.434-3.92980.19841340.14482832X-RAY DIFFRACTION98
3.9298-4.9470.1711610.12782823X-RAY DIFFRACTION98
4.947-28.63460.16141230.15822967X-RAY DIFFRACTION97

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