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- PDB-5aot: Very high resolution structure of a novel carbohydrate binding mo... -

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Basic information

Entry
Database: PDB / ID: 5aot
TitleVery high resolution structure of a novel carbohydrate binding module from Ruminococcus flavefaciens FD-1 endoglucanase Cel5A
ComponentsCarbohydrate binding module
KeywordsSUGAR BINDING PROTEN / CARBOHYDRATE BINDING MODULE / ENDOGLUCANASE CEL5A / CELLULOSOME / RUMINOCOCCUS FLAVEFACIENS FD-1 / CARBOHYDRATE ACTIVE ENZYME
Function / homologyCarbohydrate binding module-like / metal ion binding / CACODYLATE ION / Carbohydrate binding module
Function and homology information
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsPires, A.J. / Ribeiro, T. / Thompson, A. / Venditto, I. / Fernandes, V.O. / Bule, P. / Santos, H. / Alves, V.D. / Pires, V. / Ferreira, L.M.A. ...Pires, A.J. / Ribeiro, T. / Thompson, A. / Venditto, I. / Fernandes, V.O. / Bule, P. / Santos, H. / Alves, V.D. / Pires, V. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Purification and Crystallographic Studies of a Putative Carbohydrate-Binding Module from the Ruminococcus Flavefaciens Fd-1 Endoglucanase Cel5A.
Authors: Pires, A.J. / Ribeiro, T. / Thompson, A. / Venditto, I. / Fernandes, V.O. / Bule, P. / Santos, H. / Alves, V.D. / Pires, V. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionSep 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Dec 5, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbohydrate binding module
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4327
Polymers11,8351
Non-polymers5976
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.272, 45.020, 49.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbohydrate binding module / Cbm74-rfgh5


Mass: 11834.903 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, UNP RESIDUES 406-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1A9TAF4
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCACODYLATE ION (CAC): FROM THE CRYSTALLISATION BUFFER. GLYCEROL (GOL): FROM THE CRYOPROTECTANT.
Sequence detailsTRUNCATED AT C-TERMINAL WITH A HIS-TAG.

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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: 1.85 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growpH: 6.5
Details: 20 MG/ML OF PROTEIN IN 0.2 M SODIUM ACETATE, 0.1 M CACODYLIC ACID PH 6.5, 30%(W/V) POLYETHYLENE GLYCOL 8000. 30%(V/V) GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8266
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.02→33.29 Å / Num. obs: 42277 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.2
Reflection shellResolution: 1.02→1.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.5 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AOS

5aos


Resolution: 1.02→33.29 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.045 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. U VALUES REFINED INDIVIDUALLY. PDB_REDO WAS USED IN THE PENULTIMATE ROUND OF REFINEMENT FOR VALIDATION. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. U VALUES REFINED INDIVIDUALLY. PDB_REDO WAS USED IN THE PENULTIMATE ROUND OF REFINEMENT FOR VALIDATION. RESIDUES 404-409 ARE DISORDERED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17028 2472 4.9 %RANDOM
Rwork0.16443 ---
obs0.16472 47545 99.64 %-
Solvent computationVDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.359 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2---0.43 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.02→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 35 135 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019903
X-RAY DIFFRACTIONr_bond_other_d0.0020.02790
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9241232
X-RAY DIFFRACTIONr_angle_other_deg0.75731839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4765117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3625.83348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73815136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.626151
X-RAY DIFFRACTIONr_chiral_restr0.0950.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
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_it1.2771.188423
X-RAY DIFFRACTIONr_mcbond_other1.2341.183422
X-RAY DIFFRACTIONr_mcangle_it1.661.784531
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0441.446480
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_restr2.92331693
X-RAY DIFFRACTIONr_sphericity_free23.507531
X-RAY DIFFRACTIONr_sphericity_bonded11.28751770
LS refinement shellResolution: 1.018→1.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 192 -
Rwork0.446 3306 -
obs--95.13 %

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