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- PDB-4dh2: Crystal structure of Coh-OlpC(Cthe_0452)-Doc435(Cthe_0435) comple... -

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Basic information

Entry
Database: PDB / ID: 4dh2
TitleCrystal structure of Coh-OlpC(Cthe_0452)-Doc435(Cthe_0435) complex: A novel type I Cohesin-Dockerin complex from Clostridium thermocellum ATTC 27405
Components
  • Cellulosome anchoring protein cohesin region
  • Dockerin type 1
KeywordsCELL ADHESION/PROTEIN BINDING / cellulosome / cohesin / dockerin / type I cohesin-dockerin / protein-protein interaction / cell adhesion / CELL ADHESION-PROTEIN BINDING complex
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Cel124 C-terminal catalytic domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain ...: / Cel124 C-terminal catalytic domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Dockerin type 1 / Cellulosome anchoring protein cohesin region
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsAlves, V.D. / Carvalho, A.L. / Najmudin, S.H. / Bras, J. / Prates, J.A.M. / Fontes, C.M.G.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Novel Clostridium thermocellum Type I Cohesin-Dockerin Complexes Reveal a Single Binding Mode.
Authors: Bras, J.L. / Alves, V.D. / Carvalho, A.L. / Najmudin, S. / Prates, J.A. / Ferreira, L.M. / Bolam, D.N. / Romao, M.J. / Gilbert, H.J. / Fontes, C.M.
History
DepositionJan 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Cellulosome anchoring protein cohesin region
B: Dockerin type 1
C: Cellulosome anchoring protein cohesin region
D: Dockerin type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,11817
Polymers57,0934
Non-polymers1,02513
Water8,305461
1
A: Cellulosome anchoring protein cohesin region
B: Dockerin type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1079
Polymers28,5462
Non-polymers5607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-69 kcal/mol
Surface area11750 Å2
MethodPISA
2
C: Cellulosome anchoring protein cohesin region
D: Dockerin type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0118
Polymers28,5462
Non-polymers4646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-58 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.760, 90.760, 135.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cellulosome anchoring protein cohesin region


Mass: 19063.643 Da / Num. of mol.: 2 / Fragment: unp residues 99-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0452 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner cells / References: UniProt: A3DCL1
#2: Protein Dockerin type 1


Mass: 9482.773 Da / Num. of mol.: 2 / Fragment: unp residues 32-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0435 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner cells / References: UniProt: A3DCJ4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 2 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.745→78.6 Å / Num. obs: 66027 / % possible obs: 99.9 % / Redundancy: 14.9 % / Rsym value: 0.09 / Net I/σ(I): 18.7
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.887 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 65309
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.86-10044.70.342503
6.47-8.8652.20.724829
5.35-6.4752.10.7661045
4.66-5.3547.20.8031211
4.18-4.6642.50.8511353
3.83-4.1843.50.8351499
3.55-3.8346.70.8271618
3.32-3.55470.8041711
3.14-3.3246.10.8191814
2.98-3.1448.20.8131942
2.84-2.9849.50.8092010
2.72-2.8451.10.8112125
2.62-2.7250.90.8272196
2.52-2.6248.50.8472272
2.44-2.5249.90.8342365
2.36-2.4448.60.8622428
2.29-2.3647.20.862519
2.23-2.2947.50.8682559
2.17-2.23460.8842641
2.11-2.1745.60.8912694
2.06-2.1146.90.8932810
2.02-2.0646.40.8922829
1.97-2.0244.90.8952921
1.93-1.9747.30.9032971
1.89-1.9349.90.8973004
1.86-1.8949.40.8923108
1.82-1.8650.70.8863153
1.79-1.8251.50.8883179
1.75-1.7954.40.8624000

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
DM6phasing
PHENIX1.7.2_865refinement
PDB_EXTRACT3.1data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CCL

2ccl


Resolution: 1.75→39.3 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.47 / σ(F): 1.34 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 3344 5.07 %
Rwork0.181 --
obs0.183 65956 99.9 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.56 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.5604 Å20 Å2-0 Å2
2--1.5604 Å20 Å2
3----3.1207 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 49 461 4133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143854
X-RAY DIFFRACTIONf_angle_d1.2965281
X-RAY DIFFRACTIONf_dihedral_angle_d12.6171409
X-RAY DIFFRACTIONf_chiral_restr0.083575
X-RAY DIFFRACTIONf_plane_restr0.006656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.745-1.770.31941250.29242570X-RAY DIFFRACTION100
1.77-1.79640.28421510.27082533X-RAY DIFFRACTION100
1.7964-1.82440.28611430.25652605X-RAY DIFFRACTION100
1.8244-1.85440.29061460.24772565X-RAY DIFFRACTION100
1.8544-1.88630.28531390.23832582X-RAY DIFFRACTION100
1.8863-1.92060.28561410.22372578X-RAY DIFFRACTION100
1.9206-1.95760.23551560.20582558X-RAY DIFFRACTION100
1.9576-1.99750.19471370.1842575X-RAY DIFFRACTION100
1.9975-2.0410.22341320.18142605X-RAY DIFFRACTION100
2.041-2.08840.23571350.17022575X-RAY DIFFRACTION100
2.0884-2.14070.1981460.16642605X-RAY DIFFRACTION100
2.1407-2.19850.22081340.16652594X-RAY DIFFRACTION100
2.1985-2.26320.20971260.1692609X-RAY DIFFRACTION100
2.2632-2.33630.2421390.16362606X-RAY DIFFRACTION100
2.3363-2.41980.25361300.1822582X-RAY DIFFRACTION100
2.4198-2.51660.22061390.17362627X-RAY DIFFRACTION100
2.5166-2.63110.19981250.16912612X-RAY DIFFRACTION100
2.6311-2.76980.22941480.17982607X-RAY DIFFRACTION100
2.7698-2.94330.24541610.19242593X-RAY DIFFRACTION100
2.9433-3.17050.20761390.19632635X-RAY DIFFRACTION100
3.1705-3.48930.19761470.18442648X-RAY DIFFRACTION100
3.4893-3.99380.19411470.15682642X-RAY DIFFRACTION100
3.9938-5.03020.15411450.13152685X-RAY DIFFRACTION100
5.0302-39.31010.22531130.212821X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.4374 Å / Origin y: 9.5578 Å / Origin z: -9.7545 Å
111213212223313233
T0.1059 Å2-0.051 Å2-0.0139 Å2-0.1919 Å2-0.0282 Å2--0.1677 Å2
L0.0167 °2-0.0464 °20.0078 °2-0.2502 °20.0437 °2--0.5892 °2
S0.0037 Å °0.0219 Å °0.0441 Å °0.0119 Å °0.0252 Å °-0.0649 Å °-0.0385 Å °0.089 Å °0.0229 Å °
Refinement TLS groupSelection details: all

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