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- PDB-6k55: Inactivated mutant (D140A) of Hyperthermophilic GH6 cellobiohydro... -

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Basic information

Entry
Database: PDB / ID: 6k55
TitleInactivated mutant (D140A) of Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with hexasaccharide
ComponentsGlucanase
KeywordsHYDROLASE / glycoside hydrolase / GH6 / thermostable
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesArdenticatenia bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.883 Å
AuthorsBaba, S. / Takeda, M. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T.
CitationJournal: To Be Published
Title: A hyperthermophilic cellobiohydrolase mined from a hot spring metagenomic data
Authors: Takeda, M. / Baba, S. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T.
History
DepositionMay 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
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_struct_conn_angle / pdbx_validate_close_contact / 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 / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 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: Glucanase
B: Glucanase
C: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,16812
Polymers140,5633
Non-polymers3,6059
Water1,65792
1
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0564
Polymers46,8541
Non-polymers1,2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint13 kcal/mol
Surface area15300 Å2
MethodPISA
2
B: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0564
Polymers46,8541
Non-polymers1,2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint13 kcal/mol
Surface area15300 Å2
MethodPISA
3
C: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0564
Polymers46,8541
Non-polymers1,2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint13 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.949, 140.010, 110.578
Angle α, β, γ (deg.)90.00, 101.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glucanase


Mass: 46854.234 Da / Num. of mol.: 3 / Mutation: D140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ardenticatenia bacterium (bacteria) / Gene: D6802_06765 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4Y1YS11*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1b_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Sequence detailsFIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A ...FIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A LOCUS/ACCESSION NUMBER OF LC163906. D140A REPRESENTS MUTATION.

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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: 4.71 Å3/Da / Density % sol: 73.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%(w/v) PEG 1000, 0.1M sodium cacodylate (pH 6.5), 0.2M magnesium chloride, 0.5M cellohexaose (Soaking for 10 min)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.883→42.347 Å / Num. obs: 56407 / % possible obs: 96.07 % / Redundancy: 4.3 % / Biso Wilson estimate: 64.31 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.1994 / Rpim(I) all: 0.101 / Rrim(I) all: 0.2246 / Net I/σ(I): 5.66
Reflection shellResolution: 2.883→2.986 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.8245 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 4695 / CC1/2: 0.529 / Rpim(I) all: 0.5236 / Rrim(I) all: 0.983 / % possible all: 80.45

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K52

6k52


Resolution: 2.883→42.347 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.02
RfactorNum. reflection% reflection
Rfree0.218 2846 5.05 %
Rwork0.1787 --
obs0.1807 56333 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.883→42.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9917 0 240 92 10249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210453
X-RAY DIFFRACTIONf_angle_d0.64514323
X-RAY DIFFRACTIONf_dihedral_angle_d8.4458479
X-RAY DIFFRACTIONf_chiral_restr0.0461577
X-RAY DIFFRACTIONf_plane_restr0.0041895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8833-2.9330.34161010.2991909X-RAY DIFFRACTION68
2.933-2.98630.31631330.29712538X-RAY DIFFRACTION92
2.9863-3.04380.30211320.28622632X-RAY DIFFRACTION95
3.0438-3.10590.33831270.29792730X-RAY DIFFRACTION96
3.1059-3.17340.37271430.29092722X-RAY DIFFRACTION98
3.1734-3.24720.2891410.26352705X-RAY DIFFRACTION98
3.2472-3.32840.3171390.24132727X-RAY DIFFRACTION99
3.3284-3.41830.30861420.22732749X-RAY DIFFRACTION99
3.4183-3.51880.25411490.22532728X-RAY DIFFRACTION99
3.5188-3.63240.23121370.19942760X-RAY DIFFRACTION99
3.6324-3.76210.26961520.18242698X-RAY DIFFRACTION98
3.7621-3.91260.22731670.16562744X-RAY DIFFRACTION98
3.9126-4.09060.16611390.16142730X-RAY DIFFRACTION98
4.0906-4.3060.18381430.14712742X-RAY DIFFRACTION99
4.306-4.57550.1951480.14022710X-RAY DIFFRACTION98
4.5755-4.92830.16081650.1312715X-RAY DIFFRACTION98
4.9283-5.42340.18381500.14712730X-RAY DIFFRACTION98
5.4234-6.2060.18751390.15982760X-RAY DIFFRACTION98
6.206-7.81090.21751440.15692720X-RAY DIFFRACTION98
7.8109-42.35180.14971550.1372738X-RAY DIFFRACTION96

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