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- PDB-1ogo: Dex49A from Penicillium minioluteum complex with isomaltose -

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Basic information

Entry
Database: PDB / ID: 1ogo
TitleDex49A from Penicillium minioluteum complex with isomaltose
ComponentsDEXTRANASE
KeywordsHYDROLASE / DEXTRAN DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


dextranase / dextranase activity / metabolic process / extracellular region
Similarity search - Function
Dex49a from penicillium minioluteum complex, domain 1 / Dextranase, N-terminal / Glycoside hydrolase, family 49, C-terminal / Glycoside hydrolase, family 49, N-terminal domain / Dextranase, N-terminal / Isopullulanase beta-solenoid repeat / Dextranase, beta solenoid repeat / Glycosyl hydrolase family 49 / Glycosyl hydrolase family 49 N-terminal Ig-like domain / Isopullulanase beta-solenoid repeat ...Dex49a from penicillium minioluteum complex, domain 1 / Dextranase, N-terminal / Glycoside hydrolase, family 49, C-terminal / Glycoside hydrolase, family 49, N-terminal domain / Dextranase, N-terminal / Isopullulanase beta-solenoid repeat / Dextranase, beta solenoid repeat / Glycosyl hydrolase family 49 / Glycosyl hydrolase family 49 N-terminal Ig-like domain / Isopullulanase beta-solenoid repeat / Beta solenoid repeat from Dextranase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPENICILLIUM MINIOLUTEUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsLarsson, A.M. / Stahlberg, J. / Jones, T.A.
CitationJournal: Structure / Year: 2003
Title: Dextranase from Penicillium Minioluteum. Reaction Course, Crystal Structure, and Product Complex
Authors: Larsson, A.M. / Andersson, R. / Stahlberg, J. / Kenne, L. / Jones, T.A.
History
DepositionMay 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET 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

Downloads & links

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Assembly

Deposited unit
X: DEXTRANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7872
Polymers62,4451
Non-polymers3421
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.405, 103.773, 49.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DEXTRANASE / / ALPHA-1 / 6-GLUCAN-6-GLUCANOHYDROLASE


Mass: 62444.875 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PENICILLIUM MINIOLUTEUM (fungus) / Strain: HI-4 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): MP36 / Variant (production host): HIS3 / References: UniProt: P48845, dextranase
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES: MET 35 HIS, ASN 39 ALA, ASN 571 ALA, ASN 574 ALA, VAL 577 ILE

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 5.5
Details: 0.1M SODIUM ACETATE PH5.5, 0.1M NACL,10MM CACL2,20 PERCENT MMEPEG 5000, pH 5.50
Crystal grow
*PLUS
Temperature: 293 K / pH: 5.5 / Method: vapor diffusion, hanging drop / Details: Larsson, A.M., (2002) Acta Crystallogr., D58, 346.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
20.1 Msodium acetate1droppH5.5
30.1 M1dropNaCl
410 mM1dropCaCl2
520 %PEG5000 MME1reservoir
60.1 Msodium acetate1reservoirpH5.5
70.1 M1reservoirNaCl
810 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.098
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.098 Å / Relative weight: 1
ReflectionResolution: 1.65→27.5 Å / Num. obs: 71784 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.7
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 27.5 Å / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→25.73 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.09 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3613 5 %RANDOM
Rwork0.188 ---
obs-68116 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→25.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 23 508 4922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214550
X-RAY DIFFRACTIONr_bond_other_d0.0020.023844
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9216223
X-RAY DIFFRACTIONr_angle_other_deg0.79238983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025169
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02917
X-RAY DIFFRACTIONr_nbd_refined0.1890.2764
X-RAY DIFFRACTIONr_nbd_other0.2440.24669
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.22543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2384
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.52844
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10424612
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.48131706
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2714.51611
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→1.7 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 227
Rwork0.256 4753
Refinement
*PLUS
Lowest resolution: 25.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.27

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