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- PDB-1j10: beta-amylase from Bacillus cereus var. mycoides in complex with GGX -

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Basic information

Entry
Database: PDB / ID: 1j10
Titlebeta-amylase from Bacillus cereus var. mycoides in complex with GGX
ComponentsBeta-amylase
KeywordsHYDROLASE / BETA-AMYLASE / RAW-STARCH BINDING DOMAIN
Function / homology
Function and homology information


amylopectin maltohydrolase activity / beta-amylase / beta-amylase activity / starch binding / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Beta-amylase active site 2. / Beta-amylase active site 1. / Glycosyl hydrolase family 14 / Glycoside hydrolase, family 14 / Glycoside hydrolase, family 14, conserved site / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain ...Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Beta-amylase active site 2. / Beta-amylase active site 1. / Glycosyl hydrolase family 14 / Glycoside hydrolase, family 14 / Glycoside hydrolase, family 14, conserved site / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate binding module family 20 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / Immunoglobulin-like fold / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsOyama, T. / Miyake, H. / Kusunoki, M. / Nitta, Y.
Citation
Journal: J.BIOCHEM.(TOKYO) / Year: 2003
Title: Crystal Structures of beta-Amylase from Bacillus cereus var. mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents
Authors: Oyama, T. / Miyake, H. / Kusunoki, M. / Nitta, Y.
#1: Journal: J.BIOCHEM.(TOKYO) / Year: 1999
Title: Crystal Structure of beta-Amylase from Bacillus cereus var. mycoides at 2.2 A resolution
Authors: Oyama, T. / Kusunoki, M. / Kishimoto, Y. / Takasaki, Y. / Nitta, Y.
#2: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 1996
Title: Kinetic Study of Active Site Structure of beta-Amylase from Bacillus cereus var. mycoides
Authors: Nitta, Y. / Shirakawa, M. / Takasaki, Y.
History
DepositionNov 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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_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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-amylase
B: Beta-amylase
C: Beta-amylase
D: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,39016
Polymers233,4344
Non-polymers3,95612
Water10,124562
1
A: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3474
Polymers58,3591
Non-polymers9893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3474
Polymers58,3591
Non-polymers9893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3474
Polymers58,3591
Non-polymers9893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3474
Polymers58,3591
Non-polymers9893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.900, 112.900, 146.200
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Beta-amylase / / 1 / 4-alpha-D-glucan maltohydrolase


Mass: 58358.523 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacillus cereus (bacteria) / Strain: var. mycoides / References: UniProt: P36924, beta-amylase
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 474.412 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 474.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1a_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 6000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Oyama, T., (1998) Protein Pept.Lett., 5, 349.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
250 mMammonium chloride1drop
36-8 %(w/v)PEG60001reservoir
450 mMammonium chloride1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 14, 1997 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→42.6 Å / Num. obs: 154446 / % possible obs: 82.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.217 / % possible all: 60.4
Reflection
*PLUS
Redundancy: 2.1 % / Num. measured all: 322908 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 60.4 % / Redundancy: 1.6 % / Num. unique obs: 14111 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementStarting model: PDB ENTRY 5BCA
Resolution: 2.1→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 6733 -RANDOM
Rwork0.189 ---
obs-136111 85.7 %-
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16476 0 260 562 17298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.451
X-RAY DIFFRACTIONx_dihedral_angle_d21.894
X-RAY DIFFRACTIONx_improper_angle_d1.045
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.894
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.045

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