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- PDB-5bca: BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES -

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Basic information

Entry
Database: PDB / ID: 5bca
TitleBETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES
ComponentsPROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
KeywordsHYDROLASE / BETA-AMYLASE / RAW-STARCH BINDING DOMAIN
Function / homology
Function and homology information


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. / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. ...Beta-amylase, CBM20 domain / Glycoside hydrolase, family 14A, bacterial / Beta-amylase active site 2. / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-amylase / Beta-amylase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsOyama, T. / Kusunoki, M. / Kishimoto, Y. / Takasaki, Y. / Nitta, Y.
Citation
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.
#1: Journal: Protein Pept.Lett. / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of Beta-Amylase from Bacillus Cereus Var. Mycoides
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.
#3: Journal: Biosci.Biotechnol.Biochem. / Year: 1996
Title: Cloning, Sequencing, and Expression of a Beta-Amylase Gene from Bacillus Cereus Var. Mycoides and Characterization of its Products
Authors: Yamaguchi, T. / Matsumoto, Y. / Shirakawa, M. / Kibe, M. / Hibino, T. / Kozaki, S. / Takasaki, Y. / Nitta, Y.
History
DepositionMar 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
B: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
C: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
D: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,5948
Polymers233,4344
Non-polymers1604
Water13,547752
1
A: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3992
Polymers58,3591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3992
Polymers58,3591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3992
Polymers58,3591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3992
Polymers58,3591
Non-polymers401
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
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.705536, -0.458632, 0.540255), (-0.462537, 0.279566, 0.841369), (-0.536916, -0.843504, -0.01489)9.3968, 42.0681, 68.0321
2given(-0.950033, 0.071478, 0.303856), (0.085982, -0.875849, 0.474864), (0.300075, 0.477262, 0.825939)71.9516, 60.8634, -28.0591
3given(-0.869138, 0.207822, -0.448787), (0.206265, -0.672425, -0.710844), (-0.449505, -0.710391, 0.541563)86.6692, 57.9276, 51.888

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Components

#1: Protein
PROTEIN (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) / Cellular location: EXTRACELLULAR / Variant: MYCOIDES / Strain: BACILLUS CEREUS
References: UniProt: Q9Z4N9, UniProt: P36924*PLUS, beta-amylase
#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.: 752 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growpH: 9 / Details: pH 9.0
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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: PHOTON FACTORY / Detector: WEISSENBERG IMAGE PLATE / Details: BENT QUARTZ CRYSTAL
RadiationMonochromator: PHOTON FACTORY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→95.3 Å / Num. obs: 113923 / % possible obs: 81.5 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.1 / % possible all: 71.9
Reflection
*PLUS
Num. measured all: 649891
Reflection shell
*PLUS
% possible obs: 71.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.24 5370 5 %RANDOM
Rwork0.186 ---
obs-102087 74 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16476 0 4 752 17232
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7062
X-RAY DIFFRACTIONp_mcangle_it2.573
X-RAY DIFFRACTIONp_scbond_it2.0962
X-RAY DIFFRACTIONp_scangle_it3.1363
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1350.15
X-RAY DIFFRACTIONp_singtor_nbd0.1940.3
X-RAY DIFFRACTIONp_multtor_nbd0.2190.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor20.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg25.36

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