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- PDB-6fop: Glycoside hydrolase family 81 from Clostridium thermocellum (CtLa... -

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Basic information

Entry
Database: PDB / ID: 6fop
TitleGlycoside hydrolase family 81 from Clostridium thermocellum (CtLam81A), Mutant E515A
ComponentsGlycoside hydrolase family 81
KeywordsHYDROLASE / GH81 / Glycoside hydrolase / Clostridium thermocellum / glucanase / Laminarin
Function / homology
Function and homology information


glucan endo-1,3-beta-glucanase activity, C-3 substituted reducing group / polysaccharide catabolic process
Similarity search - Function
Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Glycoside hydrolase family 81
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCorreia, M.A.S.C. / Carvalho, A.L.
Funding support Portugal, 5items
OrganizationGrant numberCountry
FCTUID/Multi/04378/2013 Portugal
FCTPTDC/BBB-BEP/0869/2014 Portugal
FCTIF/01621/2013/CP1183/CT0002 Portugal
FCTPTDC/BIA-MIC/5947 Portugal
FCTPEst-C/EQB/LA0006/2013 Portugal
CitationJournal: Int.J.Biol.Macromol. / Year: 2018
Title: Novel insights into the degradation of beta-1,3-glucans by the cellulosome of Clostridium thermocellum revealed by structure and function studies of a family 81 glycoside hydrolase.
Authors: Kumar, K. / Correia, M.A.S. / Pires, V.M.R. / Dhillon, A. / Sharma, K. / Rajulapati, V. / Fontes, C.M.G.A. / Carvalho, A.L. / Goyal, A.
History
DepositionFeb 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Glycoside hydrolase family 81
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,06030
Polymers80,0011
Non-polymers2,05929
Water12,863714
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-231 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.917, 139.033, 197.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-818-

CL

21A-829-

NI

31A-917-

HOH

41A-1519-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycoside hydrolase family 81 /


Mass: 80001.039 Da / Num. of mol.: 1 / Mutation: E515A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0660 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A3DD66

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Non-polymers , 8 types, 743 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) 2-methyl-2,4-pentanediol, 0.1M sodium acetate pH4,6 and 0.02M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.4→45.15 Å / Num. obs: 166379 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.7 / Num. measured all: 1103933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.4-1.426.90.6085583881470.9042.899
7.67-45.156.60.058749811430.9943599.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K3A

4k3a


Resolution: 1.4→45.15 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.577 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1327 8356 5 %RANDOM
Rwork0.1077 ---
obs0.1089 158020 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 70.42 Å2 / Biso mean: 19.355 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å2-0 Å2
2---0.48 Å20 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 1.4→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5660 0 119 714 6493
Biso mean--34.18 33.83 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026120
X-RAY DIFFRACTIONr_bond_other_d0.0020.025560
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9458393
X-RAY DIFFRACTIONr_angle_other_deg0.959312833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41924.212273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59315921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6921517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217015
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021476
X-RAY DIFFRACTIONr_rigid_bond_restr1.625311678
X-RAY DIFFRACTIONr_sphericity_free31.5955208
X-RAY DIFFRACTIONr_sphericity_bonded10.287512004
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 645 -
Rwork0.203 11472 -
all-12117 -
obs--98.56 %

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