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- PDB-6p2m: Crystal structure of the Caldicellulosiruptor lactoaceticus GH74 ... -

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Basic information

Entry
Database: PDB / ID: 6p2m
TitleCrystal structure of the Caldicellulosiruptor lactoaceticus GH74 (ClGH74a) enzyme in complex with LLG xyloglucan
ComponentsType 3a cellulose-binding domain protein
KeywordsHYDROLASE / glycosyl hydrolase / GH74 / xyloglucanase / 7-fold beta-propeller
Function / homology
Function and homology information


xyloglucan metabolic process / hydrolase activity, acting on glycosyl bonds / cellulose binding / polysaccharide catabolic process
Similarity search - Function
: / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...: / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-PE3 / Type 3a cellulose-binding domain protein
Similarity search - Component
Biological speciesCaldicellulosiruptor lactoaceticus 6A (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsStogios, P.J. / Skarina, T. / Arnal, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74.
Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Attia, M.A. / Skarina, T. / Viborg, A.H. / Henrissat, B. / Savchenko, A. / Brumer, H.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type 3a cellulose-binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8908
Polymers74,6721
Non-polymers2,2187
Water21,2581180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.994, 72.759, 150.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Type 3a cellulose-binding domain protein


Mass: 74671.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor lactoaceticus 6A (bacteria)
Gene: Calla_2311 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2PXX7
#2: Polysaccharide beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D- ...beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1092.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-2DXylpa1-6DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-1-1-2-3-2-3/a4-b1_b4-c1_b6-f1_c6-d1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1186 molecules

#3: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1180 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (w/v) PEG3350, 0.1 M Tris pH 8.5, xyloglucan mixture

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→25 Å / Num. obs: 50820 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.063 / Net I/σ(I): 18.2
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2479 / CC1/2: 0.623 / Rpim(I) all: 0.438 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fkq

5fkq


Resolution: 1.98→24.608 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.36
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1875 3.93 %RANDOM
Rwork0.1558 ---
obs0.1576 47656 93.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→24.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 119 1180 6565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035570
X-RAY DIFFRACTIONf_angle_d0.5727610
X-RAY DIFFRACTIONf_dihedral_angle_d15.0951914
X-RAY DIFFRACTIONf_chiral_restr0.049828
X-RAY DIFFRACTIONf_plane_restr0.003962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9763-2.02970.25581300.23783109X-RAY DIFFRACTION84
2.0297-2.08940.27231380.22133238X-RAY DIFFRACTION88
2.0894-2.15680.25481370.21563334X-RAY DIFFRACTION90
2.1568-2.23380.23841360.19443376X-RAY DIFFRACTION91
2.2338-2.32320.24971380.19213488X-RAY DIFFRACTION93
2.3232-2.42880.22471400.1823462X-RAY DIFFRACTION93
2.4288-2.55680.24951380.17393478X-RAY DIFFRACTION93
2.5568-2.71680.20891500.17483557X-RAY DIFFRACTION95
2.7168-2.92620.22741480.17233603X-RAY DIFFRACTION96
2.9262-3.22010.20791490.15013638X-RAY DIFFRACTION97
3.2201-3.68470.20021540.12623739X-RAY DIFFRACTION99
3.6847-4.63730.15971540.10953803X-RAY DIFFRACTION99
4.6373-24.60970.15571630.13753956X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41950.85170.14740.7766-0.46083.9304-0.0936-0.11960.0861-0.05570.03630.0787-0.1937-0.28010.06450.18580.02090.01670.1175-0.03420.1708-22.58440.076-12.467
20.3919-0.12460.05520.643-0.01280.67320.0069-0.0602-0.00850.04240.0024-0.08140.00380.018-0.00850.1502-0.01690.00940.18250.00670.1804-8.532-3.1403-0.7636
30.79140.2211-0.40120.5408-0.26480.57330.02340.04190.0609-0.0870.023-0.01-0.0183-0.0739-0.04720.26180.00230.04390.1975-0.00510.1842-13.076114.7419-34.2407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 433 )
3X-RAY DIFFRACTION3chain 'A' and (resid 434 through 726 )

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