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- PDB-4wkz: Complex of autonomous ScaG cohesin CohG and X-doc domains -

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Basic information

Entry
Database: PDB / ID: 4wkz
TitleComplex of autonomous ScaG cohesin CohG and X-doc domains
Components
  • Autonomous cohesin
  • Putative cellulose-binding protein
KeywordsSTRUCTURAL PROTEIN / Nine-stranded beta sandwich / cohesin / X-Dockerin
Function / homology
Function and homology information


polysaccharide catabolic process / 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 / Immunoglobulin-like / Sandwich ...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 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / NITRATE ION / Putative cellulose-binding protein / Autonomous cohesin
Similarity search - Component
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.79 Å
AuthorsVoronov-Goldman, M. / Lamed, R. / Bayer, E.A. / Yaniv, O. / Shimon, L.J.W.
CitationJournal: To Be Published
Title: Complex of autonomous ScaG cohesin CohG and X-doc domains
Authors: Voronov-Goldman, M. / Lamed, R. / Bayer, E.A. / Yaniv, O. / Shimon, L.J.W.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cellulose-binding protein
B: Autonomous cohesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8467
Polymers47,5862
Non-polymers2605
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-42 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.029, 211.781, 36.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Putative cellulose-binding protein


Mass: 26535.953 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: pET28(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A0AEF5
#2: Protein Autonomous cohesin


Mass: 21049.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Plasmid: pET28(+) / Production host: Escherichia coli (E. coli) / References: UniProt: W5IDC3

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Non-polymers , 4 types, 337 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: No 37 of Crystal Screen kit from Hampton Research

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 56262 / % possible obs: 87.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.1
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 1.85

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 1.79→105.89 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.835 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22273 2124 5.2 %RANDOM
Rwork0.17851 ---
obs0.18075 38637 72.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.422 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2--0.76 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.79→105.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 14 332 3554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023360
X-RAY DIFFRACTIONr_bond_other_d0.0010.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9554576
X-RAY DIFFRACTIONr_angle_other_deg1.40837095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56126.226159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45215550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.711157
X-RAY DIFFRACTIONr_chiral_restr0.0970.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023922
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02725
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_it2.3981.6251704
X-RAY DIFFRACTIONr_mcbond_other2.3761.621701
X-RAY DIFFRACTIONr_mcangle_it3.3522.4152138
X-RAY DIFFRACTIONr_mcangle_other3.3532.4162139
X-RAY DIFFRACTIONr_scbond_it4.1652.0011656
X-RAY DIFFRACTIONr_scbond_other4.1431.9971654
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9142.8422436
X-RAY DIFFRACTIONr_long_range_B_refined7.68616.00514632
X-RAY DIFFRACTIONr_long_range_B_other7.57515.62114346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.786→1.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 73 -
Rwork0.282 1360 -
obs--34.76 %
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)
11.31970.02170.14031.6480.39481.46090.0667-0.0117-0.48640.1033-0.05940.11180.5512-0.046-0.00720.2221-0.0233-0.01250.05850.0030.194621.32229.1262.484
21.52720.0084-0.39670.88740.04722.5470.0130.00020.19920.00730.01170.002-0.2059-0.0936-0.02470.04560.006-0.01180.0154-0.00010.035226.25767.0414.486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 234
2X-RAY DIFFRACTION2B11 - 194

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