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- PDB-3v10: Crystal structure of the collagen binding domain of Erysipelothri... -

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Basic information

Entry
Database: PDB / ID: 3v10
TitleCrystal structure of the collagen binding domain of Erysipelothrix rhusiopathiae surface protein RspB
ComponentsRhusiopathiae surface protein B
KeywordsCELL ADHESION / Rhusiopathiae surface protein B / Collagen Hug model / DEv-IgG fold / Collagen binding protein
Function / homology
Function and homology information


cell wall / collagen binding / cell adhesion / extracellular region
Similarity search - Function
Collagen binding domain / Collagen binding domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Immunoglobulin-like - #740 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Prealbumin-like fold domain ...Collagen binding domain / Collagen binding domain / Collagen-binding surface protein Cna-like, B-type domain / Cna protein B-type domain / Immunoglobulin-like - #740 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Rhusiopathiae surface protein B
Similarity search - Component
Biological speciesErysipelothrix rhusiopathiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsPonnuraj, K. / Swarmistha devi, A. / Ogawa, Y. / Shimoji, Y. / Subramainan, B.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Collagen adhesin-nanoparticle interaction impairs adhesin's ligand binding mechanism
Authors: Devi, A.S. / Ogawa, Y. / Shimoji, Y. / Balakumar, S. / Ponnuraj, K.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhusiopathiae surface protein B
B: Rhusiopathiae surface protein B


Theoretical massNumber of molelcules
Total (without water)71,4022
Polymers71,4022
Non-polymers00
Water7,945441
1
A: Rhusiopathiae surface protein B


Theoretical massNumber of molelcules
Total (without water)35,7011
Polymers35,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rhusiopathiae surface protein B


Theoretical massNumber of molelcules
Total (without water)35,7011
Polymers35,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.170, 67.390, 102.410
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rhusiopathiae surface protein B


Mass: 35700.875 Da / Num. of mol.: 2 / Fragment: Collagen binding domain, UNP residues 31-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erysipelothrix rhusiopathiae (bacteria)
Gene: rspB / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q83VG5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.23 Å3/Da / Density % sol: 44.81 % / Description: STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35% PEG 2000 monomethyl ether, 100mM sodium cacodylate, 20mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.75→38 Å / Num. obs: 112956 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
Auto-Rickshawsoftware pipelinephasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1047 0.8 %Random
Rwork0.225 ---
all-124328 --
obs-112895 90.8 %-
Solvent computationBsol: 37.143 Å2
Displacement parametersBiso max: 39.3 Å2 / Biso mean: 17.5126 Å2 / Biso min: 1.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.787 Å20 Å20.761 Å2
2--0.907 Å20 Å2
3----2.694 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 0 441 5230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.2691.5
X-RAY DIFFRACTIONc_scbond_it2.1812
X-RAY DIFFRACTIONc_mcangle_it1.7382
X-RAY DIFFRACTIONc_scangle_it2.8412.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param

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