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- PDB-4v1b: Structure of a novel carbohydrate binding module from glycoside h... -

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Basic information

Entry
Database: PDB / ID: 4v1b
TitleStructure of a novel carbohydrate binding module from glycoside hydrolase family 5 glucanase from Ruminococcus flavefaciens FD-1 collected at the Zn edge
ComponentsCARBOHYDRATE BINDING MODULE
KeywordsSUGAR BINDING PROTEIN / CELLULOSOME
Function / homologyCarbohydrate binding module
Function and homology information
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 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
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-8.7 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.260, 132.260, 104.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGB WP009983134

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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
Details: 0.2 M K2SO4, 20% PEG 3350. CRYO 30% GLYCEROL IN THE ABOVE CONDITION, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2855
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2855 Å / Relative weight: 1
ReflectionResolution: 2.69→66.13 Å / Num. obs: 9947 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 19.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.1
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 19 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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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 4V18

4v18


Resolution: 2.69→66.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 27.482 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 1.285 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20339 477 4.8 %RANDOM
Rwork0.19408 ---
obs0.19451 9468 99.81 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.606 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å2-1.77 Å20 Å2
2---3.54 Å20 Å2
3---11.48 Å2
Refinement stepCycle: LAST / Resolution: 2.69→66.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 0 4 2265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022302
X-RAY DIFFRACTIONr_bond_other_d0.0020.022165
X-RAY DIFFRACTIONr_angle_refined_deg0.9921.9613116
X-RAY DIFFRACTIONr_angle_other_deg0.79835045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3295299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05127.27388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16815409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
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_it2.674.3651198
X-RAY DIFFRACTIONr_mcbond_other2.6664.3641197
X-RAY DIFFRACTIONr_mcangle_it4.1816.5421494
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8864.7941103
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: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 34 -
Rwork0.359 695 -
obs--99.59 %
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)
13.91580.3157-0.53113.7677-0.37651.6622-0.0446-0.1862-0.38540.15580.1010.0568-0.04020.0306-0.05640.28640.0235-0.01410.16480.04850.0545-3.419-21.564-35.207
24.26070.1727-0.172.95990.50082.5564-0.0351-0.612-0.44360.7150.2146-0.1673-0.1012-0.0281-0.17950.61250.037-0.09470.45680.20950.14146.445-20.921-17.553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A437 - 587
2X-RAY DIFFRACTION2B438 - 586

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