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- PDB-5aos: Structure of a novel carbohydrate binding module from Ruminococcu... -

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Basic information

Entry
Database: PDB / ID: 5aos
TitleStructure of a novel carbohydrate binding module from Ruminococcus flavefaciens FD-1 endoglucanase Cel5A solved at the As edge
ComponentsCarbohydrate binding module
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING MODULE / ENDOGLUCANASE CEL5A / CELLULOSOME / RUMINOCOCCUS FLAVEFACIENS FD-1 / CARBOHYDRATE ACTIVE ENZYME
Function / homologyCACODYLATE ION / Carbohydrate binding module
Function and homology information
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.29 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 29, 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_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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)12,3126
Polymers11,8071
Non-polymers5055
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.393, 45.214, 49.563
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


Mass: 11806.894 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, UNP RESIDUES 28-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1A9TAF3
#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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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

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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 PROTEIN IN.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: 1.04408
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04408 Å / Relative weight: 1
ReflectionResolution: 1.29→33.4 Å / Num. obs: 25196 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.1
Reflection shellResolution: 1.29→1.34 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 8.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHASERphasing
REFMAC5.8.0097refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.29→33.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.998 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. PDB_REDO WAS USED FOR VALIDATING IN THE FINAL ROUND OF REFINEMENT. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.13829 1250 5 %RANDOM
Rwork0.12592 ---
obs0.12655 23770 99.5 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.18 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.29→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 29 98 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019867
X-RAY DIFFRACTIONr_bond_other_d0.0020.02762
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9161180
X-RAY DIFFRACTIONr_angle_other_deg1.01231767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88625.55645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75415130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.942151
X-RAY DIFFRACTIONr_chiral_restr0.1280.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02211
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_it1.1450.96409
X-RAY DIFFRACTIONr_mcbond_other1.1320.954408
X-RAY DIFFRACTIONr_mcangle_it1.6351.444512
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6311.267458
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_restr3.16931629
X-RAY DIFFRACTIONr_sphericity_free24.251529
X-RAY DIFFRACTIONr_sphericity_bonded7.92951673
LS refinement shellResolution: 1.291→1.324 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.155 79 -
Rwork0.112 1676 -
obs--97.99 %

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