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- PDB-4fl4: Scaffoldin conformation and dynamics revealed by a ternary comple... -

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Basic information

Entry
Database: PDB / ID: 4fl4
TitleScaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome
Components
  • Cellulosome anchoring protein cohesin region
  • Glycoside hydrolase family 9
  • Scaffolding dockerin binding protein A
KeywordsPROTEIN BINDING / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / cohesin / dockerin / X module / cell surface / hydrolase
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Immunoglobulin-like - #4130 / Glycosyl hydrolases family 9 (GH9) active site signature 1. / Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Cellulase N-terminal ig-like domain / Immunoglobulin-like - #680 / Cellulase, Ig-like domain / : / Glycoside hydrolase family 9, His active site ...Immunoglobulin-like - #4130 / Glycosyl hydrolases family 9 (GH9) active site signature 1. / Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Cellulase N-terminal ig-like domain / Immunoglobulin-like - #680 / Cellulase, Ig-like domain / : / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Carboxypeptidase-like, regulatory domain superfamily / Clostridium cellulosome enzymes repeated domain signature. / 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. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endoglucanase D / : / : / Scaffolding dockerin binding protein A / CipA protein
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCurrie, M.A. / Adams, J.J. / Faucher, F. / Bayer, E.A. / Jia, Z. / Smith, S.P. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Scaffoldin Conformation and Dynamics Revealed by a Ternary Complex from the Clostridium thermocellum Cellulosome.
Authors: Currie, M.A. / Adams, J.J. / Faucher, F. / Bayer, E.A. / Jia, Z. / Smith, S.P.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJun 27, 2012ID: 3P0D
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Aug 22, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Glycoside hydrolase family 9
B: Scaffolding dockerin binding protein A
C: Cellulosome anchoring protein cohesin region
D: Glycoside hydrolase family 9
E: Scaffolding dockerin binding protein A
F: Cellulosome anchoring protein cohesin region
G: Glycoside hydrolase family 9
H: Scaffolding dockerin binding protein A
I: Cellulosome anchoring protein cohesin region
J: Glycoside hydrolase family 9
K: Scaffolding dockerin binding protein A
L: Cellulosome anchoring protein cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,84686
Polymers260,63312
Non-polymers6,21374
Water77543
1
A: Glycoside hydrolase family 9
B: Scaffolding dockerin binding protein A
C: Cellulosome anchoring protein cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,56720
Polymers65,1583
Non-polymers1,40917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-177 kcal/mol
Surface area24170 Å2
MethodPISA
2
D: Glycoside hydrolase family 9
E: Scaffolding dockerin binding protein A
F: Cellulosome anchoring protein cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,04825
Polymers65,1583
Non-polymers1,88922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-215 kcal/mol
Surface area24080 Å2
MethodPISA
3
G: Glycoside hydrolase family 9
H: Scaffolding dockerin binding protein A
I: Cellulosome anchoring protein cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,56720
Polymers65,1583
Non-polymers1,40917
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-164 kcal/mol
Surface area24580 Å2
MethodPISA
4
J: Glycoside hydrolase family 9
K: Scaffolding dockerin binding protein A
L: Cellulosome anchoring protein cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,66421
Polymers65,1583
Non-polymers1,50518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-206 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.374, 186.305, 191.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Glycoside hydrolase family 9


Mass: 9948.213 Da / Num. of mol.: 4 / Fragment: type I dockerin (UNP residues 584-649)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cther_2220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D1NID1, UniProt: A3DDN1*PLUS
#2: Protein
Scaffolding dockerin binding protein A


Mass: 20550.199 Da / Num. of mol.: 4 / Fragment: type II cohesin (UNP residues 27-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: sdbA / Production host: Escherichia coli (E. coli) / References: UniProt: P71143
#3: Protein
Cellulosome anchoring protein cohesin region


Mass: 34659.938 Da / Num. of mol.: 4
Fragment: type I cohesin, X module, type II dockerin (UNP residues 9-320)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: ClothDRAFT_2952 / Production host: Escherichia coli (E. coli) / References: UniProt: C7HJU1, UniProt: Q46453*PLUS

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Non-polymers , 3 types, 117 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 58 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.3-1.5 M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97927 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 105418 / Num. obs: 104697 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 73.99 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.27
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10408 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.947 Å / SU ML: 0.76 / σ(F): 1.99 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 5241 5.01 %RANDOM
Rwork0.1909 ---
obs0.1932 104690 99.64 %-
all-104697 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.818 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.1839 Å2-0 Å2-0 Å2
2---9.2404 Å20 Å2
3----6.9435 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15953 0 306 43 16302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916479
X-RAY DIFFRACTIONf_angle_d1.18922525
X-RAY DIFFRACTIONf_dihedral_angle_d15.115674
X-RAY DIFFRACTIONf_chiral_restr0.0772660
X-RAY DIFFRACTIONf_plane_restr0.0052891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83170.35541710.31373316X-RAY DIFFRACTION100
2.8317-2.8650.41611730.31023279X-RAY DIFFRACTION100
2.865-2.89980.3411740.29663276X-RAY DIFFRACTION100
2.8998-2.93640.3681740.29293273X-RAY DIFFRACTION100
2.9364-2.97490.35981560.29153295X-RAY DIFFRACTION100
2.9749-3.01550.36681740.27853300X-RAY DIFFRACTION100
3.0155-3.05840.34312120.27663265X-RAY DIFFRACTION99
3.0584-3.10390.32891770.26743250X-RAY DIFFRACTION100
3.1039-3.15220.33691690.24733323X-RAY DIFFRACTION100
3.1522-3.20370.28551530.23713284X-RAY DIFFRACTION100
3.2037-3.25870.29531590.21743343X-RAY DIFFRACTION100
3.2587-3.31770.28311770.22353298X-RAY DIFFRACTION100
3.3177-3.38120.27111610.22013279X-RAY DIFFRACTION100
3.3812-3.44990.27551880.21253252X-RAY DIFFRACTION99
3.4499-3.52450.24751740.20313324X-RAY DIFFRACTION100
3.5245-3.60610.24341810.1923299X-RAY DIFFRACTION100
3.6061-3.69570.23411710.18723274X-RAY DIFFRACTION99
3.6957-3.79490.24081610.17923290X-RAY DIFFRACTION100
3.7949-3.90580.23781740.18553254X-RAY DIFFRACTION98
3.9058-4.03090.23651780.17453308X-RAY DIFFRACTION99
4.0309-4.17370.23481540.16673343X-RAY DIFFRACTION99
4.1737-4.33920.20341640.15523339X-RAY DIFFRACTION100
4.3392-4.53440.20721820.15543302X-RAY DIFFRACTION100
4.5344-4.77040.19651840.16013354X-RAY DIFFRACTION100
4.7704-5.06470.20891840.1613314X-RAY DIFFRACTION100
5.0647-5.44840.21451870.17793353X-RAY DIFFRACTION100
5.4484-5.98320.2231760.18183364X-RAY DIFFRACTION100
5.9832-6.81850.24541840.18333358X-RAY DIFFRACTION100
6.8185-8.47940.19051820.17453423X-RAY DIFFRACTION100
8.4794-19.94760.17251870.17683517X-RAY DIFFRACTION99

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