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- PDB-4iu2: Cohesin-dockerin -X domain complex from Ruminococcus flavefacience -

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Basic information

Entry
Database: PDB / ID: 4iu2
TitleCohesin-dockerin -X domain complex from Ruminococcus flavefacience
Components
  • Cell-wall anchoring protein
  • Cellulose-binding protein
KeywordsSTRUCTURAL PROTEIN / Beta sandwich / cellulose degradation
Function / homology
Function and homology information


polysaccharide catabolic process / carbohydrate binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #3810 / Carbohydrate-binding protein CttA, X module / Cellulose-binding protein CttA, N-terminal / Cellulose-binding protein CttA N-terminal domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like ...Immunoglobulin-like - #3810 / Carbohydrate-binding protein CttA, X module / Cellulose-binding protein CttA, N-terminal / Cellulose-binding protein CttA N-terminal domain / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Putative cellulose-binding protein / Cell-wall anchoring protein
Similarity search - Component
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsSalama-Alber, O. / Bayer, E. / Frolow, F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Atypical Cohesin-Dockerin Complex Responsible for Cell Surface Attachment of Cellulosomal Components: BINDING FIDELITY, PROMISCUITY, AND STRUCTURAL BUTTRESSES.
Authors: Salama-Alber, O. / Jobby, M.K. / Chitayat, S. / Smith, S.P. / White, B.A. / Shimon, L.J. / Lamed, R. / Frolow, F. / Bayer, E.A.
History
DepositionJan 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_alt_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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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: Cell-wall anchoring protein
B: Cellulose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,25313
Polymers49,5462
Non-polymers70711
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.714, 78.714, 203.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cell-wall anchoring protein


Mass: 22946.514 Da / Num. of mol.: 1 / Fragment: UNP residues 29-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Gene: scaE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0AEF6
#2: Protein Cellulose-binding protein


Mass: 26599.607 Da / Num. of mol.: 1 / Fragment: UNP residues 565-803
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Gene: cttA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0AEF5

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Non-polymers , 4 types, 629 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, ammonium sulfate 1.8 M, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97841 Å / Relative weight: 1
ReflectionResolution: 2→20.03 Å / Num. obs: 44177 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 17.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: dev_1269)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.001→20.03 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2085 5.04 %RANDOM
Rwork0.153 ---
all0.1552 76982 --
obs0.1552 44058 93.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→20.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 31 618 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093595
X-RAY DIFFRACTIONf_angle_d0.9454938
X-RAY DIFFRACTIONf_dihedral_angle_d11.8961259
X-RAY DIFFRACTIONf_chiral_restr0.065542
X-RAY DIFFRACTIONf_plane_restr0.004643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0014-2.02580.26151260.23052434X-RAY DIFFRACTION85
2.0258-2.05150.28051580.22392292X-RAY DIFFRACTION85
2.0515-2.07850.2321430.21212431X-RAY DIFFRACTION87
2.0785-2.10690.24641400.20412414X-RAY DIFFRACTION88
2.1069-2.1370.22171080.20052552X-RAY DIFFRACTION89
2.137-2.16890.24381430.19052395X-RAY DIFFRACTION87
2.1689-2.20280.25541180.18012513X-RAY DIFFRACTION89
2.2028-2.23890.24461350.17712521X-RAY DIFFRACTION91
2.2389-2.27750.18571530.17222567X-RAY DIFFRACTION94
2.2775-2.31890.19831540.16752571X-RAY DIFFRACTION89
2.3189-2.36350.21861230.16762501X-RAY DIFFRACTION91
2.3635-2.41170.24011000.1732598X-RAY DIFFRACTION92
2.4117-2.46410.20921410.16342553X-RAY DIFFRACTION92
2.4641-2.52140.18971330.16032580X-RAY DIFFRACTION93
2.5214-2.58440.21321620.16562588X-RAY DIFFRACTION93
2.5844-2.65420.24361140.16332674X-RAY DIFFRACTION95
2.6542-2.73230.211440.16172687X-RAY DIFFRACTION96
2.7323-2.82040.21511550.16492638X-RAY DIFFRACTION96
2.8204-2.92110.21591460.15782766X-RAY DIFFRACTION97
2.9211-3.03790.21531540.16282693X-RAY DIFFRACTION97
3.0379-3.1760.17911480.14892728X-RAY DIFFRACTION98
3.176-3.34320.18571500.14882727X-RAY DIFFRACTION99
3.3432-3.55240.1811520.13912743X-RAY DIFFRACTION99
3.5524-3.82610.15951430.122802X-RAY DIFFRACTION99
3.8261-4.21010.161460.11442749X-RAY DIFFRACTION99
4.2101-4.81680.12921300.10952770X-RAY DIFFRACTION99
4.8168-6.05950.17471310.12752821X-RAY DIFFRACTION100
6.0595-28.93880.18291310.1552793X-RAY DIFFRACTION100
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)
14.1534-1.70212.21351.975-0.72931.9117-0.04210.020.23550.0395-0.011-0.0305-0.444-0.05440.11340.25670.00060.03520.168-0.02170.187674.134568.904552.7631
23.57980.28392.751.5194-1.00178.8134-0.11350.636-0.0581-0.66410.1166-0.1108-0.35060.18470.03370.38910.03570.01960.2171-0.02620.162274.770960.016530.4019
32.7653-0.70281.35141.557-0.48133.5072-0.00340.0059-0.102-0.0546-0.01840.0390.032-0.01590.01310.11020.00860.02510.10270.00180.123976.603150.535946.7686
41.3356-0.1480.16831.54450.14022.39090.03540.01090.0557-0.0851-0.04740.0307-0.235-0.06280.01810.11-0.00710.02090.1070.00490.121976.422460.408848.8172
52.6796-1.25351.10623.2871-2.1296.39130.12490.21850.2939-0.5023-0.1293-0.0063-0.6453-0.13930.06510.32380.0628-0.00440.14620.03490.219172.226170.474138.6872
64.10220.49751.05333.4512-0.31923.65930.06140.94620.7901-0.87340.1240.1707-0.595-0.08650.05920.52810.0703-0.01050.32980.14370.241971.532467.650726.6727
74.1228-1.4414-3.61341.87671.02873.38880.0323-0.4009-0.05680.3658-0.12920.32840.1626-0.16560.16990.2465-0.06520.06510.3642-0.02750.254262.186141.8319114.0259
80.6744-0.0602-0.7570.9202-0.29374.9754-0.0357-0.05080.18140.03640.01140.12590.1423-0.27260.04970.1122-0.01820.00750.24-0.00610.217262.980340.8288101.9517
92.99241.0064-2.45352.9947-1.31256.07160.2382-0.13550.17050.231-0.00710.1313-0.528-0.0031-0.21980.17580.00590.00970.19630.00350.183966.96947.735890.9494
101.3783-0.2094-0.51841.6619-0.33142.8026-0.1289-0.2103-0.21580.19930.0255-0.02010.33350.21370.04860.20070.02490.03340.190.04260.152977.983540.678369.7198
114.096-2.3689-0.80574.1323-2.80375.2171-0.0459-0.3535-0.39270.37610.361.12080.2394-0.6256-0.14320.1964-0.03610.060.29470.05450.349861.124944.945961.0794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 202 )
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 212 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 19 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 120 )
10X-RAY DIFFRACTION10chain 'B' and (resid 121 through 217 )
11X-RAY DIFFRACTION11chain 'B' and (resid 218 through 242 )

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