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- PDB-1jdd: MUTANT (E219Q) MALTOTETRAOSE-FORMING EXO-AMYLASE COCRYSTALLIZED W... -

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Basic information

Entry
Database: PDB / ID: 1jdd
TitleMUTANT (E219Q) MALTOTETRAOSE-FORMING EXO-AMYLASE COCRYSTALLIZED WITH MALTOTETRAOSE (CRYSTAL TYPE 2)
Components1,4-ALPHA MALTOTETRAHYDROLASE
KeywordsHYDROLASE / MALTOTETRAOSE-FORMING EXO AMYLASE
Function / homology
Function and homology information


glucan 1,4-alpha-maltotetraohydrolase / glucan 1,4-alpha-maltotetraohydrolase activity / starch catabolic process / starch binding / alpha-amylase activity / extracellular region / metal ion binding
Similarity search - Function
Glucan 1,4-alpha-maltotetraohydrolase, domain C / Glucan 1,4-alpha-maltotetraohydrolase, domain C / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain ...Glucan 1,4-alpha-maltotetraohydrolase, domain C / Glucan 1,4-alpha-maltotetraohydrolase, domain C / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / Glucan 1,4-alpha-maltotetraohydrolase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsYoshioka, Y. / Hasegawa, K. / Matsuura, Y. / Katsube, Y. / Kubota, M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structures of a mutant maltotetraose-forming exo-amylase cocrystallized with maltopentaose.
Authors: Yoshioka, Y. / Hasegawa, K. / Matsuura, Y. / Katsube, Y. / Kubota, M.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Crystal Structure of a Maltotetraose-Forming Exo-Amylase from Pseudomonas Stutzeri
Authors: Morishita, Y. / Hasegawa, K. / Matsuura, Y. / Katsube, Y. / Kubota, M. / Sakai, S.
History
DepositionJun 16, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-ALPHA MALTOTETRAHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1554
Polymers47,4091
Non-polymers7473
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.600, 170.700, 46.800
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 1,4-ALPHA MALTOTETRAHYDROLASE / MALTOTETRAOSE-FORMING EXO-AMYLASE


Mass: 47408.637 Da / Num. of mol.: 1 / Mutation: E219Q
Source method: isolated from a genetically manipulated source
Details: CRYSTAL TYPE 2 / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: MO-19 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P13507, glucan 1,4-alpha-maltotetraohydrolase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %(w/v)protein1drop
220 mMTris-HCl1drop
30.9 Mammonium sulfate1drop
410 mg/mlmaltopentaose1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 27, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 35190 / % possible obs: 84.6 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.089
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 102610

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 2 / Details: X-PLOR WAS ALSO USED. /
RfactorNum. reflection
Rwork0.191 -
obs-35190
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 46 227 3570
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7251
X-RAY DIFFRACTIONp_mcangle_it1.2661.5
X-RAY DIFFRACTIONp_scbond_it1.3521.5
X-RAY DIFFRACTIONp_scangle_it2.1452
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1870.15
X-RAY DIFFRACTIONp_singtor_nbd0.1870.4
X-RAY DIFFRACTIONp_multtor_nbd0.2020.4
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1810.4
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor19.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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