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- PDB-3wdh: Crystal structure of Pullulanase from Anoxybacillus sp. LM18-11 -

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Basic information

Entry
Database: PDB / ID: 3wdh
TitleCrystal structure of Pullulanase from Anoxybacillus sp. LM18-11
ComponentsType I pullulanase
KeywordsHYDROLASE / glycoside hydrolase / pullulanase
Function / homology
Function and homology information


pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2320 / Pullulanase, N1 domain / Pullulanase N1-terminal domain / : / 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 ...Immunoglobulin-like - #2320 / Pullulanase, N1 domain / Pullulanase N1-terminal domain / : / 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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / 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
Biological speciesAnoxybacillus sp. LM18-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsXu, J. / Ren, F. / Huang, C.H. / Zheng, Y. / Zhen, J. / Ko, T.P. / Chen, C.C. / Chan, H.C. / Guo, R.T. / Ma, Y. / Song, H.
CitationJournal: To be Published
Title: Cloning, Expression, Functional and Structural Studies of Pullulanase from Anoxybacillus sp. LM18-11
Authors: Xu, J. / Ren, F. / Huang, C.H. / Zheng, Y. / Zhen, J. / Chen, C.C. / Chan, H.C. / Guo, R.T. / Ma, Y. / Song, H.
History
DepositionJun 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type I pullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2132
Polymers82,1721
Non-polymers401
Water16,664925
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.895, 65.780, 90.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-940-

HOH

21A-1056-

HOH

31A-1536-

HOH

41A-1822-

HOH

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Components

#1: Protein Type I pullulanase


Mass: 82172.422 Da / Num. of mol.: 1 / Fragment: UNP residues 3-707
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus sp. LM18-11 (bacteria) / Gene: pulA / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K9L0H1, pullulanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 925 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 0.1M HEPES, pH 7.5, 7%(w/v) Polyethylene Glycol 8000, 10%(v/v) Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 83162 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 30.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→25 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.196 4046 RANDOM
Rwork0.165 --
obs0.165 80496 -
all-83040 -
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5699 0 1 925 6625
LS refinement shellResolution: 1.75→1.81 Å /
RfactorNum. reflection
Rfree0.249 338
Rwork0.202 -

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