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- PDB-5n5p: Crystal structure of Ruminococcus flavefaciens' type III complex ... -

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Basic information

Entry
Database: PDB / ID: 5n5p
TitleCrystal structure of Ruminococcus flavefaciens' type III complex containing the fifth cohesin from scaffoldin B and the dockerin from scaffoldin A
Components(Putative cellulosomal scaffoldin protein) x 2
KeywordsPROTEIN BINDING / cellulosome / cohesin / dockerin / type III cohesin-dockerin / Coh-Doc / protein-protein interaction / cell adhesion
Function / homology
Function and homology information


polysaccharide catabolic process / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Cellulosome anchoring protein, cohesin domain / Cohesin domain / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
ACETONITRILE / Putative cellulosomal scaffoldin protein / Putative cellulosomal scaffoldin protein
Similarity search - Component
Biological speciesRuminococcus flavefaciens FD-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsBule, P. / Carvalho, A.L. / Najmudin, S. / Fontes, C.M.G.A.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-MIC/5947/2014 Portugal
Fundacao para a Ciencia e a TecnologiaSFRH/BD/86821/2012 Portugal
CitationJournal: Sci Rep / Year: 2018
Title: Higher order scaffoldin assembly in Ruminococcus flavefaciens cellulosome is coordinated by a discrete cohesin-dockerin interaction.
Authors: Bule, P. / Pires, V.M.R. / Alves, V.D. / Carvalho, A.L. / Prates, J.A.M. / Ferreira, L.M.A. / Smith, S.P. / Gilbert, H.J. / Noach, I. / Bayer, E.A. / Najmudin, S. / Fontes, C.M.G.A.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cellulosomal scaffoldin protein
B: Putative cellulosomal scaffoldin protein
C: Putative cellulosomal scaffoldin protein
D: Putative cellulosomal scaffoldin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1489
Polymers46,9464
Non-polymers2015
Water4,053225
1
A: Putative cellulosomal scaffoldin protein
B: Putative cellulosomal scaffoldin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5945
Polymers23,4732
Non-polymers1213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-35 kcal/mol
Surface area10340 Å2
MethodPISA
2
C: Putative cellulosomal scaffoldin protein
D: Putative cellulosomal scaffoldin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5534
Polymers23,4732
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-34 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.093, 142.898, 46.588
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA740 - 8751 - 136
21THRTHRCC740 - 8751 - 136
12HISHISBB644 - 7301 - 87
22HISHISDD644 - 7301 - 87

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative cellulosomal scaffoldin protein


Mass: 14252.957 Da / Num. of mol.: 2
Fragment: ScaB Type III cohesin domain, UNP residues 739-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Gene: scaB / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AEF4
#2: Protein Putative cellulosomal scaffoldin protein


Mass: 9220.265 Da / Num. of mol.: 2
Fragment: ScaA Type III dockerin domain, UNP residues 648-730
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens FD-1 (bacteria)
Gene: scaA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AEF3
#3: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#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.: 225 / 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: 2.13 Å3/Da / Density % sol: 42.35 % / Mosaicity: 0.31 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES 7.5, 1.2M Sodium Citrate, 4% v/v Acetonitrile

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.82655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82655 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.868
11-h,-k,l20.132
ReflectionResolution: 1.4→47.63 Å / Num. obs: 26512 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.056.90.2940.9740.120.31899.8
8.94-47.636.70.0640.9970.0260.06999.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lxv

5lxv


Resolution: 1.98→46.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.114 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.035
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1322 5 %RANDOM
Rwork0.1819 ---
obs0.1835 25152 96.31 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 114.41 Å2 / Biso mean: 33.69 Å2 / Biso min: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1-47.34 Å20 Å2-3.05 Å2
2---5.78 Å20 Å2
3----41.55 Å2
Refinement stepCycle: final / Resolution: 1.98→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 7 225 3519
Biso mean--39.33 33.47 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023347
X-RAY DIFFRACTIONr_bond_other_d0.0020.023177
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9364563
X-RAY DIFFRACTIONr_angle_other_deg0.89337330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0695445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85527.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62815517
X-RAY DIFFRACTIONr_chiral_restr0.0760.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A80480.07
12C80480.07
21B53940.03
22D53940.03
LS refinement shellResolution: 1.976→2.027 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 61 -
Rwork0.257 947 -
all-1008 -
obs--49.34 %
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)
11.841-0.18250.50872.0977-0.1352.17630.00010.07750.1239-0.0956-0.01660.02270.07650.15080.01650.0295-0.0049-0.10370.2459-0.01020.482112.6549.86929.025
20.57870.41920.36532.1489-0.57851.98060.0339-0.0590.0070.2246-0.0816-0.09990.57050.34050.04780.3630.1192-0.09480.30820.01270.430513.84429.62647.26
31.6440.6946-0.54842.6776-0.3053.19970.0049-0.0459-0.16350.0890.0265-0.0862-0.10890.1817-0.03150.0595-0.0365-0.14130.23270.00790.438426.53769.4140.967
41.1841-0.4853-0.36491.5875-0.80312.40090.12410.00360.0068-0.2255-0.0893-0.1087-0.55880.3209-0.03480.3907-0.1519-0.11250.29470.00380.435227.55589.46122.672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A740 - 877
2X-RAY DIFFRACTION2B644 - 730
3X-RAY DIFFRACTION3C740 - 876
4X-RAY DIFFRACTION4D644 - 730

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