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- PDB-5fu4: The complexity of the Ruminococcus flavefaciens cellulosome refle... -

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Basic information

Entry
Database: PDB / ID: 5fu4
TitleThe complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition
ComponentsCBM74-RFGH5
KeywordsSUGAR BINDING PROTEIN / CELLULOSOME / CARBOHYDRATE BINDING MODULE / RUMINOCCOCUS FLAVEFACIENS / ENDOGLUCANASE CEL5A
Function / homology: / Carbohydrate binding module-like / Cbm74-rfgh5
Function and homology information
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBasle, A. / Luis, A.S. / Venditto, I. / Gilbert, H.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition.
Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M. / Dourado, C.G. / Ferreira, L.M. / Coutinho, P.M. / ...Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M. / Dourado, C.G. / Ferreira, L.M. / Coutinho, P.M. / Henrissat, B. / Knox, J.P. / Basle, A. / Najmudin, S. / Gilbert, H.J. / Willats, W.G. / Fontes, C.M.
History
DepositionJan 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Mar 28, 2018Group: 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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBM74-RFGH5
B: CBM74-RFGH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7734
Polymers23,4402
Non-polymers1,3332
Water32418
1
A: CBM74-RFGH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2242
Polymers11,7201
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CBM74-RFGH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5482
Polymers11,7201
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.430, 55.190, 44.390
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CBM74-RFGH5


Mass: 11719.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1A9TA80*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsW490A MUTANT

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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: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 25% W/V PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97959
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2→40.32 Å / Num. obs: 13038 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia23DIIdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AOT

5aot


Resolution: 2→40.32 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.802 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. W490A MUTANT
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 719 5.5 %RANDOM
Rwork0.23643 ---
obs0.23825 12306 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.52 Å2
2---0.17 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 90 18 1514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021536
X-RAY DIFFRACTIONr_bond_other_d0.0010.021342
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9992098
X-RAY DIFFRACTIONr_angle_other_deg0.88133133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6635182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9626.11967
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63715223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.927152
X-RAY DIFFRACTIONr_chiral_restr0.0940.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.912734
X-RAY DIFFRACTIONr_mcbond_other0.7151.91733
X-RAY DIFFRACTIONr_mcangle_it1.1552.862914
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9672.11802
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 43 -
Rwork0.321 897 -
obs--98.53 %
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)
13.4356-0.9368-0.01052.1208-1.52672.754-0.09640.071-0.0398-0.0312-0.0155-0.0750.08480.14950.11190.0061-0.0016-0.00090.0640.00590.07689.5-0.187120.0329
23.10711.91160.2072.7578-0.05971.78330.1269-0.0942-0.04130.1604-0.1096-0.10950.10150.1411-0.01730.01660.0066-0.01010.04170.00130.04443.9444-5.448142.6183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A412 - 503
2X-RAY DIFFRACTION2B413 - 504

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