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- PDB-5lxv: Crystal structure of Ruminococcus flavefaciens scaffoldin C cohes... -

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Basic information

Entry
Database: PDB / ID: 5lxv
TitleCrystal structure of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein
Components
  • Carbohydrate-binding protein WP_009985128
  • Scaffoldin C
KeywordsPROTEIN BINDING / cellulosome / cohesin / dockerin / type I cohesin-dockerin / Coh-Doc / protein-protein interaction
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
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 ...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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Carbohydrate-binding protein WP_009985128 / Scaffoldin C
Similarity search - Component
Biological speciesRuminococcus flavefaciens FD-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsNajmudin, S. / Bule, P. / Fontes, C.M.G.A.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao Ciencia e TecnologiaPTDC/BIA-MIC/5947/2014 Portugal
Fundacao Ciencia e TecnologiaSFRH/BD/86821/2012 Portugal
Citation
Journal: J. Biol. Chem. / Year: 2016
Title: Single Binding Mode Integration of Hemicellulose-degrading Enzymes via Adaptor Scaffoldins in Ruminococcus flavefaciens Cellulosome.
Authors: Bule, P. / Alves, V.D. / Leitao, A. / Ferreira, L.M. / Bayer, E.A. / Smith, S.P. / Gilbert, H.J. / Najmudin, S. / Fontes, C.M.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Overexpression, crystallization and preliminary X-ray characterization of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein.
Authors: Bule, P. / Ruimy-Israeli, V. / Cardoso, V. / Bayer, E.A. / Fontes, C.M. / Najmudin, S.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jan 11, 2017Group: Database references
Revision 1.4Jan 17, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scaffoldin C
B: Carbohydrate-binding protein WP_009985128
C: Scaffoldin C
D: Carbohydrate-binding protein WP_009985128
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8868
Polymers56,7264
Non-polymers1604
Water2,018112
1
A: Scaffoldin C
B: Carbohydrate-binding protein WP_009985128
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4434
Polymers28,3632
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-37 kcal/mol
Surface area10760 Å2
MethodPISA
2
C: Scaffoldin C
D: Carbohydrate-binding protein WP_009985128
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4434
Polymers28,3632
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-36 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.590, 66.730, 109.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA3 - 1724 - 173
21GLUGLUPROPROCC3 - 1724 - 173
12VALVALTYRTYRBB889 - 95324 - 88
22VALVALTYRTYRDD889 - 95324 - 88

NCS ensembles :
ID
1
2

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Components

#1: Protein Scaffoldin C


Mass: 18571.367 Da / Num. of mol.: 2 / Fragment: ScaC Type I cohesin domain, UNP residues 29-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Gene: scaC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9FCX2
#2: Protein Carbohydrate-binding protein WP_009985128


Mass: 9791.689 Da / Num. of mol.: 2 / Fragment: Doc3: Type I dockerin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1L1QK37*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.1 M potassium thiocyanate, 30% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→59.59 Å / Num. obs: 17195 / % possible obs: 97.6 % / Redundancy: 4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.08 / Net I/σ(I): 51.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.540.3210.936199.3
8.65-59.594.10.0330.964198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.11 Å31.89 Å
Translation2.11 Å31.89 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.3.11data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.2data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CCL

2ccl


Resolution: 2.4→57 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.881 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.808 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 842 4.9 %RANDOM
Rwork0.2167 ---
obs0.2188 16238 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 90.22 Å2 / Biso mean: 35.648 Å2 / Biso min: 14.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0 Å2
2--0.45 Å20 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 2.4→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 4 112 3654
Biso mean--31.03 30.18 -
Num. residues----475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023593
X-RAY DIFFRACTIONr_bond_other_d0.0020.023308
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.9534888
X-RAY DIFFRACTIONr_angle_other_deg0.75537666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3725473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95726.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.52415583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.941158
X-RAY DIFFRACTIONr_chiral_restr0.0560.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
X-RAY DIFFRACTIONr_mcbond_it0.8151.7871898
X-RAY DIFFRACTIONr_mcbond_other0.8131.7861897
X-RAY DIFFRACTIONr_mcangle_it1.4262.6742366
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88620.1
12C88620.1
21B36330.06
22D36330.06
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 68 -
Rwork0.269 1175 -
all-1243 -
obs--98.11 %
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)
14.3979-0.0186-0.19992.54560.8211.89790.0167-0.1610.7336-0.177-0.09210.0153-0.1743-0.09880.07530.03260.0162-0.02680.0197-0.02690.206563.38760.766119.414
24.01870.38261.1511.2249-0.06723.8766-0.0063-0.57680.69020.0399-0.0032-0.3373-0.07420.15180.00950.0197-0.0037-0.05770.115-0.13860.405582.80960.393127.645
32.742-0.0795-0.19612.0515-0.07631.3662-0.0599-0.0572-0.21250.0045-0.005-0.01840.1049-0.1010.06490.0241-0.0095-0.00220.03550.0680.192462.63493.876120.995
46.2949-0.14011.02942.65130.04523.10120.0486-0.26040.05030.1259-0.0841-0.40160.0850.21870.03550.0439-0.0035-0.04820.09090.11850.277382.27394.445128.457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 174
2X-RAY DIFFRACTION2B889 - 953
3X-RAY DIFFRACTION3C1 - 173
4X-RAY DIFFRACTION4D889 - 953

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