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- PDB-5jiw: Crystal structure of Thermus aquaticus amylomaltase (GH77) in com... -

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Basic information

Entry
Database: PDB / ID: 5jiw
TitleCrystal structure of Thermus aquaticus amylomaltase (GH77) in complex with a 34-meric cycloamylose
Components4-alpha-glucanotransferase
KeywordsHYDROLASE / glycoside hydrolase / TIM barrel cycloamylose
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / 4-alpha-glucanotransferase
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsRoth, C. / Bexten, N. / Weizenmann, N. / Saenger, T. / Maier, T. / Zimmermann, W. / Straeter, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Sci Adv / Year: 2017
Title: Amylose recognition and ring-size determination of amylomaltase.
Authors: Roth, C. / Weizenmann, N. / Bexten, N. / Saenger, W. / Zimmermann, W. / Maier, T. / Strater, N.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support / reflns_shell
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
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_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1885
Polymers57,2291
Non-polymers2,9594
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint57 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.600, 157.600, 112.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 4-alpha-glucanotransferase / Amylomaltase / Disproportionating enzyme / D-enzyme


Mass: 57229.047 Da / Num. of mol.: 1 / Mutation: D293A,D395N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: malQ / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O87172, 4-alpha-glucanotransferase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2774.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,17,16/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1_j4-k1_k4-l1_l4-m1_m4-n1_n4-o1_o4-p1_p4-q1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}}}}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.0 M NaKphosphate pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.73→37.2 Å / Num. obs: 74016 / % possible obs: 99.3 % / Redundancy: 18 % / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CWY

1cwy


Resolution: 1.73→37.15 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.27
RfactorNum. reflection% reflection
Rfree0.188 1946 2.66 %
Rwork0.164 --
obs0.165 73150 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 199 443 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054473
X-RAY DIFFRACTIONf_angle_d0.8076117
X-RAY DIFFRACTIONf_dihedral_angle_d15.0312614
X-RAY DIFFRACTIONf_chiral_restr0.046657
X-RAY DIFFRACTIONf_plane_restr0.005762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.77330.28081380.23515046X-RAY DIFFRACTION100
1.7733-1.82120.24591390.22115047X-RAY DIFFRACTION100
1.8212-1.87480.24251380.21165052X-RAY DIFFRACTION100
1.8748-1.93530.20151370.20095061X-RAY DIFFRACTION100
1.9353-2.00450.22381370.18885052X-RAY DIFFRACTION100
2.0045-2.08480.18491380.18135078X-RAY DIFFRACTION100
2.0848-2.17960.19091390.1775060X-RAY DIFFRACTION100
2.1796-2.29450.19611380.17155053X-RAY DIFFRACTION100
2.2945-2.43830.18661370.16785062X-RAY DIFFRACTION99
2.4383-2.62650.16371400.17015084X-RAY DIFFRACTION99
2.6265-2.89070.18821370.17285092X-RAY DIFFRACTION99
2.8907-3.30880.2131400.16715115X-RAY DIFFRACTION99
3.3088-4.16780.16531420.14485182X-RAY DIFFRACTION100
4.1678-37.15520.18181460.14545220X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4778-0.08960.20041.2349-0.12581.3390.00210.97050.1766-0.27040.0053-0.1556-0.08910.3959-0.06130.2561-0.07930.03080.50750.03610.2012-10.4408-24.9237-37.2658
22.67120.78040.54243.7453-0.35852.90770.12720.4931-0.8204-0.1273-0.16910.24090.49820.0178-0.07220.2131-0.02820.02720.3544-0.14560.5109-5.0381-43.1653-25.0518
34.00390.6924-0.73070.3621-0.0071.2002-0.0839-0.0612-0.58430.04510.0406-0.15320.17830.12790.03720.2131-0.0178-0.02920.2106-0.01240.2445-13.5558-39.1409-13.4616
41.61280.3601-0.03450.6792-0.12962.4186-0.0124-0.01070.0529-0.04940.0120.0663-0.0292-0.17870.0020.197-0.0282-0.01620.1904-0.01670.1888-33.9555-29.1113-19.1744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 231 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 232 THROUGH 286 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 287 THROUGH 386 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 387 THROUGH 500 )

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