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Basic information

Entry
Database: PDB / ID: 4v1l
TitleHigh resolution structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1
ComponentsCARBOHYDRATE BINDING MODULE
KeywordsSUGAR BINDING PROTEIN / CEL9A / CELLULOSOME
Function / homologyDomain of unknown function DUF5620 / Domain of unknown function (DUF5620) / TRIETHYLENE GLYCOL / Carbohydrate binding module
Function and homology information
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVenditto, I. / Goyal, A. / Thompson, A. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / 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.R. / Dourado, C.G. / Ferreira, L.M.A. / 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.R. / Dourado, C.G. / Ferreira, L.M.A. / Coutinho, P.M. / Henrissat, B. / Knox, J.P. / Basle, A. / Najmudin, S. / Gilbert, H.J. / Willats, W.G.T. / Fontes, C.M.G.A.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and preliminary crystallographic studies of a novel noncatalytic carbohydrate-binding module from the Ruminococcus flavefaciens cellulosome.
Authors: Venditto, I. / Goyal, A. / Thompson, A. / Ferreira, L.M. / Fontes, C.M. / Najmudin, S.
History
DepositionSep 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Apr 18, 2018Group: 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 1.4Jan 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

Downloads & links

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Assembly

Deposited unit
A: CARBOHYDRATE BINDING MODULE
B: CARBOHYDRATE BINDING MODULE
C: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,60812
Polymers45,9903
Non-polymers1,6189
Water6,323351
1
A: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7964
Polymers15,3301
Non-polymers4673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1375
Polymers15,3301
Non-polymers8074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6743
Polymers15,3301
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.250, 102.525, 109.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-2081-

HOH

21A-2082-

HOH

31B-2080-

HOH

41C-2057-

HOH

51C-2058-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein CARBOHYDRATE BINDING MODULE


Mass: 15329.945 Da / Num. of mol.: 3 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 492-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Strain: FD-1 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: A0A140UH31*PLUS

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Non-polymers , 5 types, 360 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTETRAETHYLENE GLYCOL (PG4): JUST BASED ON ELECTRON DENSITY AND IS PROBABLY AN ARTEFACT FROM THE ...TETRAETHYLENE GLYCOL (PG4): JUST BASED ON ELECTRON DENSITY AND IS PROBABLY AN ARTEFACT FROM THE EXPRESSION OR PURIFICATION PROCEDURES. HEXAETHYLENE GLYCOL (P6G): JUST BASED ON ELECTRON DENSITY AND IS PROBABLY AN ARTEFACT FROM THE EXPRESSION OR PURIFICATION PROCEDURES. TRIETHYLENE GLYCOL (PGE): JUST BASED ON ELECTRON DENSITY AND IS PROBABLY AN ARTEFACT FROM THE EXPRESSION OR PURIFICATION PROCEDURES. GLYCEROL (GOL): FROM THE CRYOPROTECTANT

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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: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 6.5
Details: 1 M SODIUM CITRATE, 0.1 M MES PH 6.5, 30% GLYCEROL WAS ADDED IN ABOVE CONDITOIN FOR TEH CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→30.19 Å / Num. obs: 58166 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.8
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V1K

4v1k


Resolution: 1.75→74.83 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.848 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. LIGAND IDENTIFIER FROM PHENIX SUITE AND PDB_REDO WERE USED DURING REFINEMENT. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17975 2898 5 %RANDOM
Rwork0.15849 ---
obs0.15956 55267 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.75 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.75→74.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 104 351 3497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023313
X-RAY DIFFRACTIONr_bond_other_d0.0060.023084
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9484469
X-RAY DIFFRACTIONr_angle_other_deg1.14137189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87426.099141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg36.663153
X-RAY DIFFRACTIONr_chiral_restr0.0830.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023712
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02727
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_it1.9391.2971609
X-RAY DIFFRACTIONr_mcbond_other1.9371.2941608
X-RAY DIFFRACTIONr_mcangle_it2.8591.9262015
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2611.9011702
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 224 -
Rwork0.313 4010 -
obs--100 %
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)
11.50010.08420.27620.89310.37851.85380.07250.07640.0204-0.0791-0.0265-0.01050.0062-0.0411-0.04610.0120.0071-0.00150.0180.01410.143137.072-23.991-8.056
21.5427-0.008-0.49271.41120.11691.0092-0.06260.03010.0003-0.04670.0639-0.10070.07970.0811-0.00130.0390.0027-0.02340.0124-0.00680.09818.085-37.206-24.883
31.5412-1.0326-0.17762.48410.04241.51380.0680.11140.0404-0.3037-0.0855-0.1535-0.00310.050.01750.0997-0.02250.03630.03760.02210.156325.389-8.483-38.177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A494 - 624
2X-RAY DIFFRACTION2B494 - 624
3X-RAY DIFFRACTION3C494 - 624

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