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- PDB-5zru: Crystal structure of Agl-KA catalytic domain -

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Basic information

Entry
Database: PDB / ID: 5zru
TitleCrystal structure of Agl-KA catalytic domain
ComponentsAlpha-1,3-glucanase
KeywordsHYDROLASE / Agl-KA GH87
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
CARDB domain / CARDB / Right handed beta helix domain / Right handed beta helix region / Carbohydrate binding module (family 35) / Parallel beta-helix repeat / Parallel beta-helix repeats / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factor 5/8 C-terminal domain, discoidin domain ...CARDB domain / CARDB / Right handed beta helix domain / Right handed beta helix region / Carbohydrate binding module (family 35) / Parallel beta-helix repeat / Parallel beta-helix repeats / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Pectin lyase fold/virulence factor / Galactose-binding-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.833 Å
AuthorsYano, S. / Makabe, K.
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structure of the catalytic unit of GH 87-type alpha-1,3-glucanase Agl-KA from Bacillus circulans.
Authors: Yano, S. / Suyotha, W. / Oguro, N. / Matsui, T. / Shiga, S. / Itoh, T. / Hibi, T. / Tanaka, Y. / Wakayama, M. / Makabe, K.
History
DepositionApr 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,3-glucanase
C: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,34222
Polymers124,4992
Non-polymers1,84420
Water20,5371140
1
A: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,21112
Polymers62,2491
Non-polymers96211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,13110
Polymers62,2491
Non-polymers8829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alpha-1,3-glucanase
hetero molecules

C: Alpha-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,34222
Polymers124,4992
Non-polymers1,84420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2740 Å2
ΔGint-163 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.247, 126.423, 80.540
Angle α, β, γ (deg.)90.00, 97.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Alpha-1,3-glucanase


Mass: 62249.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: agl / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WYG9

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Non-polymers , 5 types, 1160 molecules

#2: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1140 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 10% PEG 6000, 0.1M HEPES(pH8.5), 10mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 98671 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 13.3
Reflection shellResolution: 1.83→1.86 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.833→19.947 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.29
RfactorNum. reflection% reflection
Rfree0.1712 4962 5.03 %
Rwork0.1411 --
obs0.1426 98636 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.833→19.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8760 0 88 1140 9988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069040
X-RAY DIFFRACTIONf_angle_d0.84612296
X-RAY DIFFRACTIONf_dihedral_angle_d10.8385182
X-RAY DIFFRACTIONf_chiral_restr0.0621314
X-RAY DIFFRACTIONf_plane_restr0.0051644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8325-1.85330.20551620.16242935X-RAY DIFFRACTION94
1.8533-1.87510.22611550.15963071X-RAY DIFFRACTION96
1.8751-1.8980.19681770.15572973X-RAY DIFFRACTION97
1.898-1.9220.20391620.15623092X-RAY DIFFRACTION98
1.922-1.94720.20751530.1493032X-RAY DIFFRACTION98
1.9472-1.97390.1781610.14113173X-RAY DIFFRACTION100
1.9739-2.00210.19341480.13633101X-RAY DIFFRACTION100
2.0021-2.03190.14961360.12713173X-RAY DIFFRACTION100
2.0319-2.06360.1561610.12413125X-RAY DIFFRACTION100
2.0636-2.09740.15971930.12383093X-RAY DIFFRACTION100
2.0974-2.13360.17621740.12713151X-RAY DIFFRACTION100
2.1336-2.17230.16251600.1343131X-RAY DIFFRACTION100
2.1723-2.2140.15781590.13723142X-RAY DIFFRACTION100
2.214-2.25920.17791550.13533115X-RAY DIFFRACTION100
2.2592-2.30820.18841830.13643147X-RAY DIFFRACTION100
2.3082-2.36180.16341430.13333156X-RAY DIFFRACTION100
2.3618-2.42080.16571640.1353115X-RAY DIFFRACTION100
2.4208-2.48610.17481680.13683177X-RAY DIFFRACTION100
2.4861-2.55920.16571790.13383103X-RAY DIFFRACTION100
2.5592-2.64160.17971850.1423131X-RAY DIFFRACTION100
2.6416-2.73580.19061660.14513144X-RAY DIFFRACTION100
2.7358-2.8450.1771680.14523152X-RAY DIFFRACTION100
2.845-2.97410.1881590.14523137X-RAY DIFFRACTION100
2.9741-3.13030.15881670.1513126X-RAY DIFFRACTION100
3.1303-3.32560.18761530.15183184X-RAY DIFFRACTION100
3.3256-3.5810.16321750.13663137X-RAY DIFFRACTION100
3.581-3.93890.15141740.13413134X-RAY DIFFRACTION100
3.9389-4.50310.1451510.13313170X-RAY DIFFRACTION100
4.5031-5.6520.15751940.13483143X-RAY DIFFRACTION100
5.652-19.94860.17661770.17583211X-RAY DIFFRACTION100

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