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- PDB-5g5d: Crystal Structure of the CohScaC2-XDocCipA type II complex from C... -

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Basic information

Entry
Database: PDB / ID: 5g5d
TitleCrystal Structure of the CohScaC2-XDocCipA type II complex from Clostridium thermocellum
Components
  • CELLULOSOMAL-SCAFFOLDING PROTEIN A
  • CELLULOSOME ANCHORING PROTEIN COHESIN REGION
KeywordsCARBOHYDRATE BINDING PROTEIN / COHESIN-DOCKERIN COMPLEX / TYPE II INTERACTION / SCAFFOLDIN / CELLULOSOME / C. THERMOCELLUM
Function / homology
Function and homology information


S-layer / 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 / : / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology (SLH) domain profile. ...Carboxypeptidase-like, regulatory domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / : / S-layer homology domain / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carboxypeptidase-like, regulatory domain superfamily / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 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. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Cellulosomal-scaffolding protein A / Cell surface glycoprotein 2
Similarity search - Component
Biological speciesRUMINICLOSTRIDIUM THERMOCELLUM AD2 (bacteria)
CLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCarvalho, A.L. / A Bras, J.L. / Najmudin, S.H. / Pinheiro, B.A. / Fontes, C.M.G.A.
CitationJournal: Sci Rep / Year: 2016
Title: Diverse specificity of cellulosome attachment to the bacterial cell surface.
Authors: Bras, J.L. / Pinheiro, B.A. / Cameron, K. / Cuskin, F. / Viegas, A. / Najmudin, S. / Bule, P. / Pires, V.M. / Romao, M.J. / Bayer, E.A. / Spencer, H.L. / Smith, S. / Gilbert, H.J. / Alves, V. ...Authors: Bras, J.L. / Pinheiro, B.A. / Cameron, K. / Cuskin, F. / Viegas, A. / Najmudin, S. / Bule, P. / Pires, V.M. / Romao, M.J. / Bayer, E.A. / Spencer, H.L. / Smith, S. / Gilbert, H.J. / Alves, V.D. / Carvalho, A.L. / Fontes, C.M.
History
DepositionMay 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_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_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: CELLULOSOME ANCHORING PROTEIN COHESIN REGION
B: CELLULOSOMAL-SCAFFOLDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8074
Polymers36,7272
Non-polymers802
Water00
1
A: CELLULOSOME ANCHORING PROTEIN COHESIN REGION


Theoretical massNumber of molelcules
Total (without water)18,9481
Polymers18,9481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULOSOMAL-SCAFFOLDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8593
Polymers17,7791
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.360, 125.805, 130.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CELLULOSOME ANCHORING PROTEIN COHESIN REGION


Mass: 18947.541 Da / Num. of mol.: 1 / Fragment: SECOND COHESIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUMINICLOSTRIDIUM THERMOCELLUM AD2 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A0A0U3TQ90, UniProt: Q06853*PLUS
#2: Protein CELLULOSOMAL-SCAFFOLDING PROTEIN A / CELLULOSE-INTEGRATING PROTEIN A / CELLULOSOMAL GLYCOPROTEIN S1/SL / COHESIN


Mass: 17779.150 Da / Num. of mol.: 1 / Fragment: DOCKERIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q06851
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Sequence detailsTHE FIRST 3 RESIDUES WERE INTRODUCED FROM THE VECTOR. THE FIRST 4 AND LAST FIVE RESIDUES ARE NOT ...THE FIRST 3 RESIDUES WERE INTRODUCED FROM THE VECTOR. THE FIRST 4 AND LAST FIVE RESIDUES ARE NOT OBSERVED IN THE ELECTRON DENSITY. A 19 RESIDUE TAG WAS INTRODUCED IN THE N-TERMINAL. THE 25 RESIDUES FROM THE N_TERMINAL ARE NOT OBSERVED IN ELECTRON DENSITY AS WELL THE LAST C-TERMINAL RESIDUE.

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 0.2M CACL2 0.1M HEPES 7.5 25% PEG4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95372
DetectorType: PILATUS / Detector: PIXEL / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.89→90.57 Å / Num. obs: 10000 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.9
Reflection shellResolution: 3→3.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.5 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BM3

2bm3


Resolution: 3→90.56 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.87 / SU B: 62.591 / SU ML: 0.488 / Cross valid method: THROUGHOUT / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30308 937 10.5 %RANDOM
Rwork0.25555 ---
obs0.26065 7968 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 3→90.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 2 0 2422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022473
X-RAY DIFFRACTIONr_bond_other_d0.0020.022386
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.963362
X-RAY DIFFRACTIONr_angle_other_deg1.01235492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7825.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4715413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.704157
X-RAY DIFFRACTIONr_chiral_restr0.1270.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022783
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
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_it0.3324.7961262
X-RAY DIFFRACTIONr_mcbond_other0.3324.7941261
X-RAY DIFFRACTIONr_mcangle_it0.6057.1921574
X-RAY DIFFRACTIONr_mcangle_other0.6047.1941575
X-RAY DIFFRACTIONr_scbond_it0.2644.8541211
X-RAY DIFFRACTIONr_scbond_other0.2644.8541211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4957.2591789
X-RAY DIFFRACTIONr_long_range_B_refined2.47745.51110000
X-RAY DIFFRACTIONr_long_range_B_other2.47745.5079999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 75 -
Rwork0.37 572 -
obs--99.08 %
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)
14.0385-0.04270.27313.00260.88456.1882-0.190.0078-0.41730.1438-0.01680.33681.3836-1.34660.20680.3397-0.33490.08860.4943-0.1080.126-12.259-11.906-9.884
25.1166-2.2354-1.09362.58630.86811.569-0.15760.834-0.47510.10830.1464-0.09490.5281-0.03130.01120.3342-0.13890.0320.5495-0.26380.13787.102-17.025-32.735
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 163
2X-RAY DIFFRACTION2B27 - 163

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