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- PDB-4v17: Structure of a novel carbohydrate binding module from glycoside h... -

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Basic information

Entry
Database: PDB / ID: 4v17
TitleStructure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1
ComponentsCARBOHYDRATE BINDING MODULE
KeywordsSUGAR BINDING PROTEIN
Function / homologyCarbohydrate binding module
Function and homology information
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVenditto, I. / Centeno, M.S.J. / 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.,Sect.F / Year: 2014
Title: Expression, Purification and Crystallization of a Novel Carbohydrate-Binding Module from the Ruminococcus Flavefaciens Cellulosome.
Authors: Venditto, I. / Centeno, M.S.J. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionSep 25, 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 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBOHYDRATE BINDING MODULE
B: CARBOHYDRATE BINDING MODULE


Theoretical massNumber of molelcules
Total (without water)34,5462
Polymers34,5462
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-14.2 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.093, 131.093, 105.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2067-

HOH

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Components

#1: Protein CARBOHYDRATE BINDING MODULE


Mass: 17273.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Strain: FD-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0A140UH28*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5
Details: 1.2 M NA2 CITRATE, 0.1 M HEPES PH 7.5 CRYO 30% GLYCEROL IN ABOVE CONDITION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→30.17 Å / Num. obs: 26385 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 16.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 15.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMET DERIVATIVE FROM 2.28 A

Resolution: 2→77.16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 11.653 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22875 1200 5.1 %RANDOM
Rwork0.20269 ---
obs0.20403 22333 99.76 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.336 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 2→77.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 85 2374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022327
X-RAY DIFFRACTIONr_bond_other_d0.0030.022180
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9553148
X-RAY DIFFRACTIONr_angle_other_deg0.86835079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53427.14391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21615412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022607
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02449
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_it2.6622.0751209
X-RAY DIFFRACTIONr_mcbond_other2.6622.0731208
X-RAY DIFFRACTIONr_mcangle_it4.0843.11509
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7052.4421117
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
Rfree0.347 91 -
Rwork0.28 1637 -
obs--99.71 %
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)
12.6757-0.0253-0.33591.9539-0.5251.32280.0073-0.0707-0.43420.1409-0.01070.1995-0.0144-0.00940.00350.13350.00140.03010.00250.00230.6825-3.494-21.383-35.537
21.9185-0.19170.21021.98920.29821.9865-0.0576-0.4196-0.34470.54730.0979-0.0882-0.04920.0436-0.04030.35390.0179-0.00630.14570.17810.72186.786-20.473-17.925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A437 - 590
2X-RAY DIFFRACTION2B439 - 587

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