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- PDB-6k54: Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex w... -

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Basic information

Entry
Database: PDB / ID: 6k54
TitleHyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with trisaccharide
ComponentsGH6 cellobiohydrolase, HMCEL6A
KeywordsHYDROLASE / glycoside hydrolase / GH6 / thermostable
Function / homology1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / beta-cellotriose / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.905 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: Novel hyperthermophilic cellobiohydrolase II isolated from hot spring microbial community
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 / 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_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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_symmetry / _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 2.2Nov 20, 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: GH6 cellobiohydrolase, HMCEL6A
B: GH6 cellobiohydrolase, HMCEL6A
C: GH6 cellobiohydrolase, HMCEL6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,54326
Polymers140,6953
Non-polymers3,84823
Water27,9591552
1
A: GH6 cellobiohydrolase, HMCEL6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,00411
Polymers46,8981
Non-polymers2,10610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area16080 Å2
MethodPISA
2
B: GH6 cellobiohydrolase, HMCEL6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8118
Polymers46,8981
Non-polymers9137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area16160 Å2
MethodPISA
3
C: GH6 cellobiohydrolase, HMCEL6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7277
Polymers46,8981
Non-polymers8296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.582, 138.699, 110.636
Angle α, β, γ (deg.)90.00, 101.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

21B-1098-

HOH

31C-874-

HOH

41C-999-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein GH6 cellobiohydrolase, HMCEL6A


Mass: 46898.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
References: cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 2 types, 4 molecules

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


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 1571 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1552 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsFIRST MET IS INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A ...FIRST MET IS INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A LOCUS/ACCESSION NUMBER OF LC163906.

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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: 4.55 Å3/Da / Density % sol: 72.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (w/v) PEG1000, 0.2M calcium acetate, 0.1M imidazole (pH 8.0), 0.5mM cellotriose

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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: Oct 29, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.905→35.944 Å / Num. obs: 194529 / % possible obs: 99.26 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1267 / Rpim(I) all: 0.05279 / Rrim(I) all: 0.1375 / Net I/σ(I): 17.78
Reflection shellResolution: 1.905→1.973 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 109980 / CC1/2: 0.716 / Rpim(I) all: 0.4462 / % possible all: 94.47

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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: 1.905→35.944 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 9732 5.01 %
Rwork0.1756 --
obs0.1769 194298 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.905→35.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9927 0 249 1552 11728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710518
X-RAY DIFFRACTIONf_angle_d0.85814382
X-RAY DIFFRACTIONf_dihedral_angle_d18.7143924
X-RAY DIFFRACTIONf_chiral_restr0.0551554
X-RAY DIFFRACTIONf_plane_restr0.0051917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9049-1.92660.32972760.31235144X-RAY DIFFRACTION83
1.9266-1.94920.30553080.28176167X-RAY DIFFRACTION100
1.9492-1.9730.29093280.26156162X-RAY DIFFRACTION100
1.973-1.9980.26543140.24136178X-RAY DIFFRACTION100
1.998-2.02420.25623390.22996134X-RAY DIFFRACTION100
2.0242-2.0520.25883390.22426162X-RAY DIFFRACTION100
2.052-2.08130.25213200.22086204X-RAY DIFFRACTION100
2.0813-2.11230.25243350.22656145X-RAY DIFFRACTION100
2.1123-2.14540.27043450.21646114X-RAY DIFFRACTION100
2.1454-2.18050.2263060.20356200X-RAY DIFFRACTION100
2.1805-2.21810.23613110.20386226X-RAY DIFFRACTION100
2.2181-2.25840.24323210.20536160X-RAY DIFFRACTION100
2.2584-2.30190.21593190.2026198X-RAY DIFFRACTION100
2.3019-2.34890.24933450.20536132X-RAY DIFFRACTION100
2.3489-2.39990.23513240.20756187X-RAY DIFFRACTION100
2.3999-2.45570.24023140.19426166X-RAY DIFFRACTION100
2.4557-2.51710.21743080.18946201X-RAY DIFFRACTION100
2.5171-2.58520.21133450.19336173X-RAY DIFFRACTION100
2.5852-2.66120.22443470.19196141X-RAY DIFFRACTION100
2.6612-2.74710.24153230.19686220X-RAY DIFFRACTION100
2.7471-2.84520.22793480.18966147X-RAY DIFFRACTION100
2.8452-2.95910.24242970.19146201X-RAY DIFFRACTION100
2.9591-3.09370.20893270.18846160X-RAY DIFFRACTION100
3.0937-3.25670.22253180.17486234X-RAY DIFFRACTION100
3.2567-3.46060.17873390.15956201X-RAY DIFFRACTION100
3.4606-3.72750.16693180.14316226X-RAY DIFFRACTION100
3.7275-4.10220.14033100.12786252X-RAY DIFFRACTION100
4.1022-4.69470.13613410.11726172X-RAY DIFFRACTION100
4.6947-5.91050.14143330.1296259X-RAY DIFFRACTION100
5.9105-35.94990.13963340.13796300X-RAY DIFFRACTION99

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