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- PDB-2guy: Orthorhombic crystal structure (space group P21212) of Aspergillu... -

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Basic information

Entry
Database: PDB / ID: 2guy
TitleOrthorhombic crystal structure (space group P21212) of Aspergillus niger alpha-amylase at 1.6 A resolution
ComponentsAlpha-amylase A
KeywordsHYDROLASE / (beta-alpha) 8 barrel
Function / homology
Function and homology information


cell wall-bounded periplasmic space / hyphal septin band / spitzenkorper / fungal-type cell wall / alpha-amylase / cell septum / carbohydrate catabolic process / alpha-amylase activity / calcium ion binding / extracellular region
Similarity search - Function
Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / 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 / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-amylase A type-1/2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsVujicic Zagar, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution.
Authors: Vujicic-Zagar, A. / Dijkstra, B.W.
History
DepositionMay 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Currently there is no aminoacid sequence database reference available for the protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-amylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1533
Polymers52,5261
Non-polymers6272
Water10,160564
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.799, 63.228, 74.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1252-

HOH

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Components

#1: Protein Alpha-amylase A / Taka-amylase A / TAA / 1 / 4- alpha-D-glucan glucanohydrolase


Mass: 52525.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus oryzae (mold) / References: UniProt: P0C1B3, alpha-amylase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 30% PEG 8000, 0.2M Na-acetate, 0.1M Na-cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91835 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91835 Å / Relative weight: 1
ReflectionResolution: 1.59→40 Å / Num. all: 65130 / Num. obs: 65130 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079
Reflection shellResolution: 1.59→1.66 Å / Rmerge(I) obs: 0.556 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDCdata collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7TAA

7taa


Resolution: 1.59→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.205 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19623 3245 5.1 %RANDOM
Rwork0.16362 ---
all0.16527 60711 --
obs0.16527 60711 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 40 564 4290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223828
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9525234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71125.115174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72515567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1041510
X-RAY DIFFRACTIONr_chiral_restr0.110.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022950
X-RAY DIFFRACTIONr_nbd_refined0.2170.31903
X-RAY DIFFRACTIONr_nbtor_refined0.3240.52703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.5815
X-RAY DIFFRACTIONr_metal_ion_refined0.030.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.598
X-RAY DIFFRACTIONr_mcbond_it1.15822394
X-RAY DIFFRACTIONr_mcangle_it1.72633805
X-RAY DIFFRACTIONr_scbond_it1.48221659
X-RAY DIFFRACTIONr_scangle_it2.12931429
LS refinement shellResolution: 1.59→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 183 -
Rwork0.252 3418 -
obs--74.8 %
Refinement TLS params.Method: refined / Origin x: 21.5739 Å / Origin y: 6.5953 Å / Origin z: 18.7641 Å
111213212223313233
T-0.0168 Å20.0354 Å20.016 Å2--0.0169 Å2-0.0221 Å2---0.0373 Å2
L1.0247 °2-0.3997 °20.0484 °2-0.8174 °2-0.2453 °2--0.6026 °2
S0.1099 Å °0.1992 Å °0.0083 Å °-0.0613 Å °-0.1166 Å °-0.0204 Å °-0.0035 Å °-0.0366 Å °0.0068 Å °

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