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- PDB-4v1k: SeMet structure of a novel carbohydrate binding module from glyco... -

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Basic information

Entry
Database: PDB / ID: 4v1k
TitleSeMet structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1
ComponentsCARBOHYDRATE BINDING MODULE
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING MODULE / GLYCOSIDE HYDROLASE FAMILY 9 / CEL9A / CELLULOSOME / RUMINOCOCCUS FLAVEFACIENS FD-1
Function / homologyDomain of unknown function DUF5620 / Domain of unknown function (DUF5620) / 2-HYDROXY BUTANE-1,4-DIOL / Carbohydrate binding module
Function and homology information
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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.,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 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 1.3Feb 7, 2018Group: Database references / Refinement description / Source and taxonomy
Category: citation / entity_src_gen / software
Item: _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_gen.pdbx_host_org_vector / _entity_src_gen.plasmid_name / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3937
Polymers15,4711
Non-polymers9226
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.051, 104.051, 104.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1629-

CA

21A-2009-

HOH

31A-2085-

HOH

41A-2086-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CARBOHYDRATE BINDING MODULE


Mass: 15470.633 Da / Num. of mol.: 1 / Fragment: RESIDUES 492-629
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE DERIVATIVE / Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Strain: FD-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: A0A140UH31*PLUS

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Non-polymers , 5 types, 150 molecules

#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-BGQ / 2-HYDROXY BUTANE-1,4-DIOL


Mass: 105.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSELENOMETHIONINE DERIVATIVE

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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: 2.89 Å3/Da / Density % sol: 58 %
Description: DATA WAS ALSO COLLECTED AT THE SE-PEAK EDGE WITH AN INVERSE BEAM.
Crystal growpH: 7
Details: 0.2 M AMMONIUM ACETATE, 1.5 M K2HPO4, 1.5 M NAH2PO4 CRYO USED WAS PARATONE-N., pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95372
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.6→42.48 Å / Num. obs: 24839 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
XDSdata scaling
SHELXDEphasing
CCP4SUITESphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→42.48 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.383 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15221 1653 6.8 %RANDOM
Rwork0.11747 ---
obs0.11986 22809 98.5 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.386 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 56 144 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021149
X-RAY DIFFRACTIONr_bond_other_d0.0010.021081
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.971549
X-RAY DIFFRACTIONr_angle_other_deg0.83332530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06326.2548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57715191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg37.546151
X-RAY DIFFRACTIONr_chiral_restr0.1140.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021271
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02244
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_it1.9982.119546
X-RAY DIFFRACTIONr_mcbond_other1.9742.113545
X-RAY DIFFRACTIONr_mcangle_it2.7473.193687
X-RAY DIFFRACTIONr_mcangle_other2.7563.202688
X-RAY DIFFRACTIONr_scbond_it3.0642.729602
X-RAY DIFFRACTIONr_scbond_other3.0642.732603
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6623.841854
X-RAY DIFFRACTIONr_long_range_B_refined4.63219.8371314
X-RAY DIFFRACTIONr_long_range_B_other4.62819.8381314
X-RAY DIFFRACTIONr_rigid_bond_restr3.79232228
X-RAY DIFFRACTIONr_sphericity_free22.299546
X-RAY DIFFRACTIONr_sphericity_bonded10.93652301
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 114 -
Rwork0.153 1591 -
obs--94.72 %
Refinement TLS params.Method: refined / Origin x: 43.6473 Å / Origin y: 66.4378 Å / Origin z: 76.4152 Å
111213212223313233
T0.0014 Å2-0.0002 Å2-0.0001 Å2-0.0006 Å2-0.0002 Å2--0.0014 Å2
L0.1106 °20.0223 °2-0.0869 °2-0.0544 °2-0.0237 °2--0.1217 °2
S-0.0078 Å °0.0028 Å °-0.0083 Å °-0.0015 Å °0.0051 Å °0.0002 Å °0.0077 Å °0 Å °0.0027 Å °

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