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- PDB-7p1z: Novel GH12 endogluconase from Aspergillus cervinus -

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Basic information

Entry
Database: PDB / ID: 7p1z
TitleNovel GH12 endogluconase from Aspergillus cervinus
ComponentsGlycoside hydrolase
KeywordsHYDROLASE / Glycoside hydrolases hydrolysis glycosidic bonds
Function / homologyACETATE ION / : / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAspergillus cervinus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsLazarenko, V.A. / Rykov, S.V. / Nikolaeva, A.Y. / Berezina, O.V. / Akentyev, F.I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2019-1658 Russian Federation
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2022
Title: Unusual substrate specificity in GH family 12: structure-function analysis of glucanases Bgh12A and Xgh12B from Aspergillus cervinus, and Egh12 from Thielavia terrestris.
Authors: Rykov, S.V. / Selimzyanova, A.I. / Nikolaeva, A.Y. / Lazarenko, V.A. / Tsurin, N.V. / Akentyev, P.I. / Zverlov, V.V. / Liebl, W. / Schwarz, W.H. / Berezina, O.V.
History
DepositionJul 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Source and taxonomy / Structure summary
Category: citation / database_2 ...citation / database_2 / entity_src_gen / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycoside hydrolase
C: Glycoside hydrolase
A: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,48411
Polymers76,9853
Non-polymers4998
Water6,449358
1
B: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7212
Polymers25,6621
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8864
Polymers25,6621
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8785
Polymers25,6621
Non-polymers2164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.094, 118.364, 125.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-907-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
32B
42A
53C
63A

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEUBA6 - 2276 - 227
211SERSERLEULEUCB6 - 2276 - 227
322SERSERASNASNBA6 - 2266 - 226
422SERSERASNASNAC6 - 2266 - 226
533GLNGLNASNASNCB5 - 2265 - 226
633GLNGLNASNASNAC5 - 2265 - 226

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Glycoside hydrolase /


Mass: 25661.615 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus cervinus (mold) / Production host: Komagataella pastoris (fungus) / Strain (production host): X33
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion / Details: Peg 6000 18,5% 0.2M CaCl2 0.1M NaAcetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.17→125.7 Å / Num. obs: 37115 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.095 / Rrim(I) all: 0.18 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.95-125.75.50.0466260.9890.0290.054
2.17-2.246.10.71531440.8660.4750.862

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GM3

5gm3


Resolution: 2.17→62.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.163 / SU B: 7.664 / SU ML: 0.179 / Average fsc free: 0.8598 / Average fsc work: 0.8791 / Cross valid method: FREE R-VALUE / ESU R: 0.264 / ESU R Free: 0.202 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2305 1893 5.107 %
Rwork0.1835 35176 -
all0.186 --
obs-37069 99.389 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.421 Å2
Baniso -1Baniso -2Baniso -3
1-7.06 Å20 Å20 Å2
2---3.219 Å20 Å2
3----3.841 Å2
Refinement stepCycle: LAST / Resolution: 2.17→62.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5120 0 32 358 5510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0115311
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.6187270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5115671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60524.4225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75515714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.415154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024116
X-RAY DIFFRACTIONr_nbd_refined0.2170.22503
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2318
X-RAY DIFFRACTIONr_metal_ion_refined0.530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2860.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.216
X-RAY DIFFRACTIONr_mcbond_it2.4713.0022693
X-RAY DIFFRACTIONr_mcangle_it3.484.4923354
X-RAY DIFFRACTIONr_scbond_it3.1752.9892618
X-RAY DIFFRACTIONr_scangle_it3.9214.433915
X-RAY DIFFRACTIONr_lrange_it5.78540.4598559
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.057470
X-RAY DIFFRACTIONr_ncsr_local_group_20.070.057494
X-RAY DIFFRACTIONr_ncsr_local_group_30.0510.057614
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.073520.0501
12CX-RAY DIFFRACTIONLocal ncs0.073520.0501
23BX-RAY DIFFRACTIONLocal ncs0.069720.0501
24AX-RAY DIFFRACTIONLocal ncs0.069720.0501
35CX-RAY DIFFRACTIONLocal ncs0.051260.05011
36AX-RAY DIFFRACTIONLocal ncs0.051260.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.2260.3321150.2752561X-RAY DIFFRACTION99.0378
2.226-2.2870.3041240.2612493X-RAY DIFFRACTION98.9788
2.287-2.3540.271370.2412422X-RAY DIFFRACTION99.0708
2.354-2.4260.3061270.2342363X-RAY DIFFRACTION99.0848
2.426-2.5050.3361190.2372266X-RAY DIFFRACTION99.5409
2.505-2.5930.2811140.2082236X-RAY DIFFRACTION99.4078
2.593-2.6910.2771090.2062165X-RAY DIFFRACTION99.4751
2.691-2.8010.2361310.2042035X-RAY DIFFRACTION99.7697
2.801-2.9250.231040.1762005X-RAY DIFFRACTION99.6221
2.925-3.0680.223840.1651923X-RAY DIFFRACTION99.4056
3.068-3.2340.216930.1541815X-RAY DIFFRACTION99.5825
3.234-3.4290.195980.1531720X-RAY DIFFRACTION99.7805
3.429-3.6660.1981040.1571601X-RAY DIFFRACTION99.359
3.666-3.9590.262860.1541529X-RAY DIFFRACTION99.6299
3.959-4.3360.185840.1441395X-RAY DIFFRACTION99.5289
4.336-4.8460.163800.1351271X-RAY DIFFRACTION99.7048
4.846-5.5930.19660.1711143X-RAY DIFFRACTION99.5881
5.593-6.8430.259440.186984X-RAY DIFFRACTION99.3237
6.843-9.6470.24500.188779X-RAY DIFFRACTION99.2814
9.647-62.930.241240.248470X-RAY DIFFRACTION98.6028

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