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- PDB-2wan: Pullulanase from Bacillus acidopullulyticus -

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Basic information

Entry
Database: PDB / ID: 2wan
TitlePullulanase from Bacillus acidopullulyticus
ComponentsPULLULANASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / POLYSACCHARIDE / AMYLASE / STARCH / CARBOHYDRATE
Function / homology
Function and homology information


Rab geranylgeranyltransferase alpha-subunit, insert domain / Golgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS ACIDOPULLULYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.65 Å
AuthorsTurkenburg, J.P. / Brzozowski, A.M. / Svendsen, A. / Borchert, T.V. / Davies, G.J. / Wilson, K.S.
CitationJournal: Proteins / Year: 2009
Title: Structure of a Pullulanase from Bacillus Acidopullulyticus.
Authors: Turkenburg, J.P. / Brzozowski, A.M. / Svendsen, A. / Borchert, T.V. / Davies, G.J. / Wilson, K.S.
History
DepositionFeb 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PULLULANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,99017
Polymers101,6331
Non-polymers1,35716
Water17,601977
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.431, 61.983, 109.668
Angle α, β, γ (deg.)90.00, 109.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PULLULANASE


Mass: 101633.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A588 CYS MODELLED AS OXIDISED CYSTEINE (CSX) / Source: (gene. exp.) BACILLUS ACIDOPULLULYTICUS (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: pullulanase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growDetails: 25-35% AS (V/V OF SATURATED SOLUTION), 0.1 M ACETATE BUFFER PH 4.5, 5-10 MM NDSB 195, OR 256, OR DETERGENT SB12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.65→104 Å / Num. obs: 124792 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.5 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.65→105.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.692 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE N-TERMINAL 111 RESIDUES IN THE SEQUENCE HAVE NOT BEEN MODELLED. THE ELECTRON DENSITY IS UNINTERPRETABLE, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE N-TERMINAL 111 RESIDUES IN THE SEQUENCE HAVE NOT BEEN MODELLED. THE ELECTRON DENSITY IS UNINTERPRETABLE, ALTHOUGH IT HAS SOME FEATURES INDICATING THIS DOMAIN IS DISORDERED BUT PRESENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.21035 6035 5.1 %RANDOM
Rwork0.17504 ---
obs0.17681 112593 95.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.218 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.16 Å2
2--0.48 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6283 0 84 977 7344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9479081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21725.931317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.961151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1491517
X-RAY DIFFRACTIONr_chiral_restr0.0830.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.23068
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24441
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2756
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3681.54121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11726690
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.43332527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9874.52370
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 437 -
Rwork0.276 7555 -
obs--87.55 %

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