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- PDB-3kcp: Crystal structure of interacting Clostridium thermocellum multimo... -

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Basic information

Entry
Database: PDB / ID: 3kcp
TitleCrystal structure of interacting Clostridium thermocellum multimodular components
Components
  • Cellulosomal-scaffolding protein A
  • Cellulosome anchoring protein, cohesin region
KeywordsSTRUCTURAL PROTEIN / Cohesin / Dockerin / X-module / Cellulosome / Carbohydrate metabolism / Cell wall biogenesis/degradation / Cellulose degradation / Glycoprotein / Polysaccharide degradation / Secreted
Function / homology
Function and homology information


cellulose binding / polysaccharide catabolic process / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / carbohydrate binding / extracellular region
Similarity search - Function
Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / : / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. ...Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / : / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / 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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cellulosome anchoring protein cohesin region / Cellulosomal-scaffolding protein A
Similarity search - Component
Biological speciesClostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsAdams, J.J. / Currie, M.A. / Bayer, E.A. / Jia, Z. / Smith, S.P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Insights into Higher-Order Organization of the Cellulosome Revealed by a Dissect-and-Build Approach: Crystal Structure of Interacting Clostridium thermocellum Multimodular Components
Authors: Adams, J.J. / Currie, M.A. / Ali, S. / Bayer, E.A. / Jia, Z. / Smith, S.P.
History
DepositionOct 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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.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_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

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Assembly

Deposited unit
A: Cellulosomal-scaffolding protein A
B: Cellulosome anchoring protein, cohesin region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3425
Polymers55,2262
Non-polymers1163
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-13.2 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.977, 58.019, 56.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is the asymmetric unit

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Components

#1: Protein Cellulosomal-scaffolding protein A / Cellulosomal glycoprotein S1/SL / Cellulose-integrating protein A / Cohesin


Mass: 34659.938 Da / Num. of mol.: 1
Fragment: Cohesin 9 and Dockerin 1-2 domains: UNP residues 1542-1853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum ATCC 27405 (bacteria)
Strain: ATCC 27405 / DSM 1237 / Gene: cipA, Cthe_3077 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06851
#2: Protein Cellulosome anchoring protein, cohesin region


Mass: 20566.199 Da / Num. of mol.: 1 / Fragment: UNP residues 27-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum ATCC 27405 (bacteria)
Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_1307, SdbA / Production host: Escherichia coli (E. coli) / References: UniProt: A3DF10
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 200 mM Ammonium sulfate, 30% w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 2005
RadiationMonochromator: Horizontal bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.94→42.49 Å / Num. all: 41456 / Num. obs: 41456 / % possible obs: 98.67 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 9.6
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4056 / Rsym value: 0.424 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
ARP/wARPmodel building
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→42.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.656 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.161 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23109 2087 5 %RANDOM
Rwork0.20567 ---
all0.20697 41456 --
obs0.20567 39350 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.94→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 3 244 3789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223609
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9674907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21325.724152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6251510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022719
X-RAY DIFFRACTIONr_nbd_refined0.2130.21630
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2263
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.215
X-RAY DIFFRACTIONr_mcbond_it1.1451.52366
X-RAY DIFFRACTIONr_mcangle_it1.79223742
X-RAY DIFFRACTIONr_scbond_it2.86331405
X-RAY DIFFRACTIONr_scangle_it4.2074.51165
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 149 -
Rwork0.253 2513 -
obs--88.17 %

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