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- PDB-3qgv: Crystal structure of a thermostable amylase variant -

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Basic information

Entry
Database: PDB / ID: 3qgv
TitleCrystal structure of a thermostable amylase variant
ComponentsAlpha amylase
KeywordsHYDROLASE / (Beta/alpha)8-barrel / alpha-amylase / family 13 glycosyl
Function / homology
Function and homology information


Golgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
sucrose / beta-cyclodextrin
Similarity search - Component
Biological speciesPyrococcus woesei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHein, K.L. / Ganshaw, G. / Bott, R. / Nissen, P.
CitationJournal: To be Published
Title: Structure of a highly mutated, thermostable \xCE\xB1-amylase variant
Authors: Hein, K.L. / Ganshaw, G. / Bott, R. / Nissen, P.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,96111
Polymers49,6801
Non-polymers2,28210
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 59.900, 272.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha amylase


Mass: 49679.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus woesei (archaea) / References: alpha-amylase

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Sugars , 2 types, 3 molecules

#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 198 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5 and 20% (v/v) Ethanol or 0.2 M Sodium-chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 55280 / Num. obs: 55126 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Ice5data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / SU ML: 0.25 / σ(F): 1.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 2779 5.04 %RANDOM
Rwork0.1646 ---
all0.1668 ---
obs0.1668 55125 99.71 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.706 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5931 Å20 Å2-0 Å2
2--6.5931 Å2-0 Å2
3----13.1862 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 141 191 3863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083867
X-RAY DIFFRACTIONf_angle_d1.2945313
X-RAY DIFFRACTIONf_dihedral_angle_d27.7681467
X-RAY DIFFRACTIONf_chiral_restr0.101546
X-RAY DIFFRACTIONf_plane_restr0.005652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13620.3041410.25272633X-RAY DIFFRACTION99
2.1362-2.1750.3271400.24022581X-RAY DIFFRACTION100
2.175-2.21690.27371380.23372654X-RAY DIFFRACTION100
2.2169-2.26210.28831330.24692570X-RAY DIFFRACTION99
2.2621-2.31130.3311440.21792648X-RAY DIFFRACTION100
2.3113-2.36510.25391380.2052595X-RAY DIFFRACTION100
2.3651-2.42420.24061370.18492642X-RAY DIFFRACTION100
2.4242-2.48980.2521410.19452621X-RAY DIFFRACTION100
2.4898-2.5630.22771370.16832590X-RAY DIFFRACTION100
2.563-2.64580.19851370.16252618X-RAY DIFFRACTION100
2.6458-2.74030.28321420.17012641X-RAY DIFFRACTION100
2.7403-2.850.21841350.17212635X-RAY DIFFRACTION100
2.85-2.97970.21971390.16082590X-RAY DIFFRACTION100
2.9797-3.13680.25091420.15612647X-RAY DIFFRACTION100
3.1368-3.33330.19231360.15512593X-RAY DIFFRACTION100
3.3333-3.59060.19181390.15092591X-RAY DIFFRACTION100
3.5906-3.95180.19811380.14612653X-RAY DIFFRACTION100
3.9518-4.52330.17041390.1272599X-RAY DIFFRACTION100
4.5233-5.69760.15611440.13272621X-RAY DIFFRACTION100
5.6976-50.01490.14741390.16862624X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.2225 Å / Origin y: -13.6966 Å / Origin z: -15.4898 Å
111213212223313233
T0.1454 Å2-0.0234 Å20.0084 Å2-0.2589 Å20.0265 Å2--0.2653 Å2
L0.5337 °2-0.3938 °20.4422 °2-0.8615 °2-0.9689 °2--3.2072 °2
S-0.0335 Å °-0.032 Å °-0.0106 Å °0.0925 Å °0.136 Å °0.037 Å °-0.0289 Å °-0.3114 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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