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- PDB-4d3l: SeMet structure of a novel carbohydrate binding module from glyco... -

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Basic information

Entry
Database: PDB / ID: 4d3l
TitleSeMet structure of a novel carbohydrate binding module from glycoside hydrolase family 9 (Cel9A) from Ruminococcus flavefaciens FD-1 in the orthorhombic form
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) / (3S)-3-HYDROXYHEPTANEDIOIC ACID / DI(HYDROXYETHYL)ETHER / Carbohydrate binding module
Function and homology information
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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: 2015
Title: Crystallization and Preliminary Crystallographic Studies of a Novel, Non-Catalytic Carbohydrate- Binding Module from Ruminococcus Flavefaciens Cellulosome.
Authors: Venditto, I. / Goyal, A. / Thompson, A. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionOct 22, 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 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)47,88612
Polymers46,4123
Non-polymers1,4749
Water4,234235
1
A: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2304
Polymers15,4711
Non-polymers7593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7094
Polymers15,4711
Non-polymers2383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9474
Polymers15,4711
Non-polymers4773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.302, 103.345, 109.067
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-2040-

HOH

21A-2057-

HOH

31B-2004-

HOH

41B-2045-

HOH

51C-2004-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein CARBOHYDRATE BINDING MODULE


Mass: 15470.633 Da / Num. of mol.: 3 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 492-629
Source method: isolated from a genetically manipulated source
Details: SELENO-METHIONINE DERIVATIVE / 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 , 9 types, 244 molecules

#2: Chemical ChemComp-2PE / NONAETHYLENE 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


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-HHD / (3S)-3-HYDROXYHEPTANEDIOIC ACID


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsNONAETHYLENE GLYCOL (2PE): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ...NONAETHYLENE GLYCOL (2PE): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ON ELECTRON DENSITY. DI(HYDROXYETHYL)ETHER (PEG): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ON ELECTRON DENSITY. TETRAETHYLENE GLYCOL (PG4): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ON ELECTRON DENSITY. HEXAETHYLENE GLYCOL (P6G): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ON ELECTRON DENSITY. CALCIUM ION (CA): POSSIBLY FROM STORAGE BUFFER. 3-HYDROXY-HEXANEDIOIC ACID (HHD): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ON ELECTRON DENSITY AT THE 3-FOLD NCS. DERIVED FROM ARGININE RESIDUE WHICH WAS ONE OF THE BEST FITS OBTAINED BY RUNNING LIGAND_IDENTIFIER IN PHENIX. DOES NOT CORRESPOND TO THE ELECTRON DENSITY IN WWPDB ENTRIES 4V1K OR 4V1L. GLYCEROL (GOL): FROM THE CRYOPROTECTANT. 1,2-ETHANEDIOL (EDO): ARTEFACT FROM EXPRESSION, PURIFICATION OR CRYSTALLISATION. BASED PURELY ON ELECTRON DENSITY.
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: 3.19 Å3/Da / Density % sol: 61 % / Description: PHASER SAD AND PARROT WERE ALSO USED.
Crystal growpH: 7
Details: 0.2 M SODIUM CITRATE, 2 M AMMONIUM SULPHATE. CRYOPROTECTANT USED PARATONE N, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2→43.63 Å / Num. obs: 37050 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 0.9 / % possible all: 69.9

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Processing

Software
NameVersionClassification
PARROTmodel building
Aimlessdata scaling
SHELXphasing
CCP4SUITESphasing
PHASERSADphasing
PARROTphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→75.02 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.187 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED WITH EACH MONOMER DEFINED AS A SINLGE TLS GROUP. PDB_REDO WAS USED IN TH PENULTIMATE REFINEMET ROUND.
RfactorNum. reflection% reflectionSelection details
Rfree0.24523 1848 5 %RANDOM
Rwork0.21201 ---
obs0.21362 35182 93.62 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.81 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→75.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 77 235 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023281
X-RAY DIFFRACTIONr_bond_other_d0.0050.023030
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9474435
X-RAY DIFFRACTIONr_angle_other_deg1.03737056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99226.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86815547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.194153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023709
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02722
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_it1.8562.4831610
X-RAY DIFFRACTIONr_mcbond_other1.8572.4791608
X-RAY DIFFRACTIONr_mcangle_it2.7513.7052015
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6432.8491669
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: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 83 -
Rwork0.392 1731 -
obs--62.57 %
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)
10.8104-0.17350.70940.55590.42151.59590.09690.06770.0354-0.057-0.0578-0.02130.03820.0216-0.03920.01570.0104-0.01040.00980.00810.196237.229-23.833-7.556
21.5540.1584-0.66480.94820.27751.0716-0.14490.0980.0284-0.04890.1547-0.04010.02680.059-0.00980.0175-0.0141-0.01720.0339-0.01850.1238.448-37.426-24.989
31.0189-1.0734-0.21812.1431-0.67691.12030.08780.03520.0734-0.3186-0.062-0.15830.1444-0.063-0.02580.07310.01390.0350.02720.02830.161525.221-8.34-38.082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A494 - 625
2X-RAY DIFFRACTION2B494 - 624
3X-RAY DIFFRACTION3C494 - 624

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