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Basic information

Entry
Database: PDB / ID: 6sav
TitleStructural and functional characterisation of three novel fungal amylases with enhanced stability and pH tolerance
Components(Alpha-amylase) x 2
KeywordsHYDROLASE / biotechnology / fungal amylase
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / calcium ion binding
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 / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily ...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 / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhizomucor pusillus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRoth, C. / Moroz, O.V. / Turkenburg, J.P. / Blagova, E. / Waterman, J. / Ariza, A. / Ming, L. / Tianqi, S. / Andersen, C. / Davies, G.J. / Wilson, K.S.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Structural and Functional Characterization of Three Novel Fungal Amylases with Enhanced Stability and pH Tolerance.
Authors: Roth, C. / Moroz, O.V. / Turkenburg, J.P. / Blagova, E. / Waterman, J. / Ariza, A. / Ming, L. / Tianqi, S. / Andersen, C. / Davies, G.J. / Wilson, K.S.
History
DepositionJul 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-amylase
B: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,21517
Polymers96,5392
Non-polymers1,67715
Water16,988943
1
A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9027
Polymers48,2691
Non-polymers6346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,31310
Polymers48,2701
Non-polymers1,0439
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.217, 62.600, 66.807
Angle α, β, γ (deg.)77.030, 81.040, 89.620
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha-amylase


Mass: 48268.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor pusillus (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: M9TI89, alpha-amylase
#2: Protein Alpha-amylase


Mass: 48269.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor pusillus (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: M9TI89, alpha-amylase

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Sugars , 1 types, 3 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 955 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.2 M NaCl, 0.1 M Na-acetate pH 4.6, 30 %MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0004 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.4→43.21 Å / Num. obs: 146177 / % possible obs: 92.9 % / Redundancy: 2.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.03 / Rrim(I) all: 0.044 / Net I/σ(I): 9.6 / Num. measured all: 315876 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.420.2491010348790.8910.2250.3372.361.9
7.67-43.210.0218158760.9960.0190.02819.390.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2taa

2taa


Resolution: 1.4→39.99 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.92 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1644 7328 5 %RANDOM
Rwork0.1363 ---
obs0.1377 138848 92.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.22 Å2 / Biso mean: 12.475 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20.28 Å2-0.2 Å2
2---0.14 Å2-0.07 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.4→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6803 0 109 943 7855
Biso mean--24.37 24.22 -
Num. residues----874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0137582
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176430
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.64510390
X-RAY DIFFRACTIONr_angle_other_deg1.6581.58715044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49321.754268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67515997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0761521
X-RAY DIFFRACTIONr_chiral_restr0.1060.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028930
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021656
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 374 -
Rwork0.221 7209 -
all-7583 -
obs--65 %

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