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- PDB-1h3g: Cyclomaltodextrinase from Flavobacterium sp. No. 92: from DNA seq... -

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Basic information

Entry
Database: PDB / ID: 1h3g
TitleCyclomaltodextrinase from Flavobacterium sp. No. 92: from DNA sequence to protein structure
ComponentsCyclomaltodextrinase
KeywordsHYDROLASE / CYCLOMALTODEXTRINASE / GLYCOSIDASE
Function / homology
Function and homology information


cyclomaltodextrinase / cyclomaltodextrinase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Cyclomaltodextrinase, N-terminal / Cyclo-malto-dextrinase, C-terminal / Cyclomaltodextrinase, N-terminal / Cyclo-malto-dextrinase C-terminal domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Cyclomaltodextrinase, N-terminal / Cyclo-malto-dextrinase, C-terminal / Cyclomaltodextrinase, N-terminal / Cyclo-malto-dextrinase C-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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cyclomaltodextrinase
Similarity search - Component
Biological speciesFlavobacterium sp. 92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsFritzsche, H.B. / Schwede, T. / Jelakovic, S. / Schulz, G.E.
CitationJournal: Eur.J.Biochem. / Year: 2003
Title: Covalent and Three-Dimensional Structure of the Cyclodextrinase from Flavobacterium Sp. No. 92.
Authors: Fritzsche, H.B. / Schwede, T. / Schulz, G.E.
History
DepositionSep 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity / entity_name_com / entity_src_gen / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _diffrn_source.pdbx_synchrotron_site ..._citation.page_last / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details
Revision 1.4Jul 10, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Nov 20, 2024Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_entry_details.has_protein_modification / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclomaltodextrinase
B: Cyclomaltodextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6806
Polymers138,5202
Non-polymers1604
Water12,484693
1
A: Cyclomaltodextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3403
Polymers69,2601
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Cyclomaltodextrinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3403
Polymers69,2601
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)181.339, 181.339, 231.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.450916, 0.849463, -0.274019), (0.851073, -0.501707, -0.154804), (-0.268978, -0.163407, -0.949183)
Vector: 46.0989, -48.7896, 91.8113)

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Components

#1: Protein Cyclomaltodextrinase


Mass: 69259.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. 92 (bacteria) / Gene: cdase / Plasmid: PET22B+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KKG0, cyclomaltodextrinase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDEGRADATION OF CYCLODEXTRINS AND LINEAR MALTOOLIGOSACCHARIDES, HYDROLIZATION OF DIFFERENT ...DEGRADATION OF CYCLODEXTRINS AND LINEAR MALTOOLIGOSACCHARIDES, HYDROLIZATION OF DIFFERENT MALTOOLIGOSACCHARIDES: GREATEST ACTIVITY FOR LINEAR MALTOOLIGOSACCHARIDES OF 5 OR 6 GLUCOSE MOIETIES AND ALSO FOR CYCLODEXTRINS,TIM-BARREL ENZYME
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: 2.74 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
250 mMHEPES1reservoirpH7.5
33.8 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9393
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 3, 2001 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL FOCUSSING / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.1→21 Å / Num. obs: 86572 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Redundancy: 7.3 % / Num. measured all: 629678 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.08 Å / % possible obs: 99.9 % / Redundancy: 7.3 % / Num. unique obs: 8625 / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→21.1 Å / SU B: 6.4 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.17
Details: FIRST CNS WAS USED FOR REFINEMENT FOLLOWED BY TLS REFINEMENT IN REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1990 2.5 %RANDOM
Rwork0.188 ---
obs0.189 78154 91.6 %-
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å2-1.07 Å20 Å2
2---2.14 Å20 Å2
3---3.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9542 0 4 693 10239
Refinement
*PLUS
Lowest resolution: 21 Å / Num. reflection obs: 78164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.016
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.34
LS refinement shell
*PLUS
Highest resolution: 2.08 Å / Lowest resolution: 2.13 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.219 / Num. reflection obs: 4817

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