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- PDB-1gcy: HIGH RESOLUTION CRYSTAL STRUCTURE OF MALTOTETRAOSE-FORMING EXO-AMYLASE -

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Basic information

Entry
Database: PDB / ID: 1gcy
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF MALTOTETRAOSE-FORMING EXO-AMYLASE
ComponentsGLUCAN 1,4-ALPHA-MALTOTETRAHYDROLASE
KeywordsHYDROLASE / BETA-ALPHA-BARREL / BETA SHEET
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
Glucan 1,4-alpha-maltotetraohydrolase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMezaki, Y. / Katsuya, Y. / Kubota, M. / Matsuura, Y.
Citation
Journal: Biosci.Biotechnol.Biochem. / Year: 2001
Title: Crystallization and structural analysis of intact maltotetraose-forming exo-amylase from Pseudomonas stutzeri.
Authors: Mezaki, Y. / Katsuya, Y. / Kubota, M. / Matsuura, Y.
#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.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Crystal Structure of a Mutant Maltotetraose-forming Exo-amylase Cocrystallized with Maltopentaose
Authors: Yoshioka, Y. / Hasegawa, K. / Matsuura, Y. / Katsube, Y. / Kubota, M.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,8493
Polymers57,7691
Non-polymers802
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.420, 171.660, 46.350
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 GLUCAN 1,4-ALPHA-MALTOTETRAHYDROLASE


Mass: 57769.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe C-terminal raw-starch binding domain of about a hundred amino acids is disordered in the crystal.
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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125.7 mg/mlprotein1drop
220 mMTris-HCl1drop
30.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.834
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 66492 / % possible obs: 89.6 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.061
Reflection
*PLUS
Num. measured all: 222219

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AMG

2amg


Resolution: 1.6→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.304 3332 5.1 %RANDOM
Rwork0.259 ---
obs0.259 65731 89.6 %-
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 2 222 3503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_mcbond_it1.471.5
X-RAY DIFFRACTIONx_mcangle_it2.172
X-RAY DIFFRACTIONx_scbond_it2.542
X-RAY DIFFRACTIONx_scangle_it3.592.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 436 4.9 %
Rwork0.315 8543 -
obs--74.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68

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