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- PDB-2y3n: Type II cohesin-dockerin domain from Bacteroides cellolosolvens -

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Basic information

Entry
Database: PDB / ID: 2y3n
TitleType II cohesin-dockerin domain from Bacteroides cellolosolvens
Components
  • CELLULOSOMAL FAMILY-48 PROCESSIVE GLYCOSIDE HYDROLASE
  • CELLULOSOMAL SCAFFOLDIN
KeywordsSTRUCTRUAL PROTEIN/HYDROLASE / STRUCTRUAL PROTEIN-HYDROLASE COMPLEX / CELLULOSOME
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulase activity / cellulose catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region / metal ion binding
Similarity search - Function
Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Type 1 dockerin domain / Dockerin domain / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain ...Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Type 1 dockerin domain / Dockerin domain / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cellulose 1,4-beta-cellobiosidase / Cellulosomal scaffoldin
Similarity search - Component
Biological speciesBACTEROIDES CELLULOSOLVENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsViegas, A. / Carvalho, A.L. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A.
CitationJournal: To be Published
Title: Type II Cohesin-Dockerin Domain from Bacteroides Cellolosolvens
Authors: Viegas, A. / Carvalho, A.L. / Prates, J.A.M. / Romao, M.J. / Fontes, C.M.G.A.
History
DepositionDec 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: CELLULOSOMAL SCAFFOLDIN
B: CELLULOSOMAL FAMILY-48 PROCESSIVE GLYCOSIDE HYDROLASE
C: CELLULOSOMAL SCAFFOLDIN
D: CELLULOSOMAL FAMILY-48 PROCESSIVE GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3028
Polymers55,1424
Non-polymers1604
Water5,386299
1
C: CELLULOSOMAL SCAFFOLDIN
D: CELLULOSOMAL FAMILY-48 PROCESSIVE GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6514
Polymers27,5712
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-27 kcal/mol
Surface area10020 Å2
MethodPISA
2
A: CELLULOSOMAL SCAFFOLDIN
B: CELLULOSOMAL FAMILY-48 PROCESSIVE GLYCOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6514
Polymers27,5712
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-28.9 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.410, 116.120, 45.160
Angle α, β, γ (deg.)90.00, 112.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CELLULOSOMAL SCAFFOLDIN / TYPE II COHESIN-DOCKERIN


Mass: 20030.451 Da / Num. of mol.: 2 / Fragment: RESIDUES 2073-2242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES CELLULOSOLVENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9FDJ9
#2: Protein CELLULOSOMAL FAMILY-48 PROCESSIVE GLYCOSIDE HYDROLASE / TYPE II COHESIN-DOCKERIN


Mass: 7540.627 Da / Num. of mol.: 2 / Fragment: RESIDUES 683-752
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES CELLULOSOLVENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6UB36
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 1.91 Å3/Da / Density % sol: 35.67 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9735
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.9→41.74 Å / Num. obs: 27197 / % possible obs: 83.7 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.5
Reflection shellResolution: 1.9→41.74 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TYJ

1tyj


Resolution: 1.9→41.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.713 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22491 1364 5 %RANDOM
Rwork0.16329 ---
obs0.16641 25833 83.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.086 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.28 Å2
2--0 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 4 299 3765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9554758
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01526.026151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01215602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.542156
X-RAY DIFFRACTIONr_chiral_restr0.1240.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212622
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.41.52231
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29223577
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.57531289
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4114.51181
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 67 -
Rwork0.165 1272 -
obs--56.83 %
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)
10.528-0.10870.74460.3841-0.4191.18940.03140.05010.0077-0.0674-0.0192-0.0260.03160.0428-0.01220.15510.0039-0.02170.12410.00250.0516-13.24426.195-20.378
20.4548-0.15610.3260.3254-0.34990.8020.0215-0.006-0.0436-0.03860.00060.01520.0512-0.064-0.02220.15350.0007-0.02560.10450.00370.0654-14.55821.324-13.606
30.9992-0.26730.57060.6041-0.34050.67910.02470.1361-0.0048-0.0452-0.0032-0.0647-0.12560.1996-0.02150.1445-0.0083-0.02640.106-0.00450.0728-9.68531.249-18.094
48.8775-2.2091-5.97017.74992.8943.3889-0.0557-0.22940.01480.06130.1543-0.05990.03030.1446-0.09860.17360.0522-0.04280.14650.01290.0224-23.96126.30810.858
51.6475-1.9998-0.12672.08240.14872.3257-0.0789-0.11810.00780.12760.0872-0.0015-0.15150.042-0.00820.1816-0.0481-0.00790.1435-0.0210.0525-13.9621.6353.752
62.9778-2.3736-4.90033.03046.28328.0349-0.2795-1.1688-0.28140.44240.171-0.06870.1130.50790.10850.45110.0643-0.07490.4410.11350.0067-15.18111.10611.76
72.4167-3.85820.43569.1412-1.49221.174-0.0437-0.0674-0.04390.03180.22710.3757-0.1357-0.2731-0.18340.11120.02260.0110.10980.0340.0823-21.69718.4582.171
81.04960.30290.05910.5996-0.11480.2878-0.0048-0.02350.05620.00190.00460.0169-0.0022-0.00490.00020.1112-0.0049-0.01990.0979-0.01540.1097-3.017-4.8192.659
91.73390.5833-0.90290.37110.0050.8105-0.01110.0826-0.02720.02720.047-0.01990.0475-0.0572-0.0360.0971-0.0261-0.01370.11280.00750.1226-8.915-18.9243.29
100.64510.87560.07551.4456-0.20470.40530.02190.0204-0.09920.0050.0185-0.20060.08130.0768-0.04040.0845-0.0022-0.01730.1156-0.00280.12955.007-13.2413.088
116.2932-2.0481-1.06859.5114-4.19793.71830.0403-0.23080.27211.3975-0.0970.56070.57480.60520.05670.50640.07630.16010.1838-0.02870.03559.691-10.383-23.761
121.14842.64941.06266.17143.97942.118-0.13720.1561-0.0451-0.64440.4819-0.4764-0.38350.2385-0.34470.1767-0.05480.09910.1726-0.05590.160511.583-4.353-11.344
1320.126717.65857.668814.52715.30932.2046-0.45360.26541.0027-0.94920.26760.0794-0.1797-0.16130.18590.45350.09630.25930.1570.07530.30687.9824.48-14.352
146.5433-16.2523-17.393924.4721-0.554223.88260.58860.39941.6153-1.241.2591-2.72620.1531-2.7571-1.84770.0583-0.0880.08080.2773-0.00460.38862.147-9.998-16.006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 48
2X-RAY DIFFRACTION2A49 - 152
3X-RAY DIFFRACTION3A153 - 175
4X-RAY DIFFRACTION4B1 - 7
5X-RAY DIFFRACTION5B8 - 27
6X-RAY DIFFRACTION6B28 - 47
7X-RAY DIFFRACTION7B48 - 66
8X-RAY DIFFRACTION8C3 - 123
9X-RAY DIFFRACTION9C124 - 138
10X-RAY DIFFRACTION10C139 - 173
11X-RAY DIFFRACTION11D1 - 6
12X-RAY DIFFRACTION12D7 - 28
13X-RAY DIFFRACTION13D29 - 59
14X-RAY DIFFRACTION14D60 - 64

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