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- PDB-7lgr: Streptococcus mutans Collagen binding Protein CNM - N2 Domain -

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Basic information

Entry
Database: PDB / ID: 7lgr
TitleStreptococcus mutans Collagen binding Protein CNM - N2 Domain
ComponentsCollagen-binding adhesin
KeywordsCELL ADHESION / Streptococcus mutans / CNM / C-terminal N2 Domain / Collagen binding
Function / homology
Function and homology information


collagen binding / cell adhesion / extracellular region / membrane
Similarity search - Function
Collagen binding domain / Collagen binding domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Collagen-binding adhesin
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchormann, N. / Deivanayagam, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01 DE29007 United States
CitationJournal: To Be Published
Title: Streptococcus mutans Collagen binding Protein CNM - Structural and Functional Analysis of the C-terminal N2 Domain
Authors: Schormann, N. / Deivanayagam, C.
History
DepositionJan 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen-binding adhesin


Theoretical massNumber of molelcules
Total (without water)19,7241
Polymers19,7241
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.553, 48.553, 106.424
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Collagen-binding adhesin


Mass: 19724.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: cnm / Plasmid: pET-23d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): OneShot / References: UniProt: B9A875
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.8 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 1.5M ammonium sulfate, 100mM sodium acetate, pH 4.5 or 100mM citric acid, pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→42.05 Å / Num. obs: 19890 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.039 / Rrim(I) all: 0.126 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 10.7 % / Rmerge(I) obs: 2.175 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 961 / CC1/2: 0.699 / Rpim(I) all: 0.699 / Rrim(I) all: 2.286 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6A

2f6a


Resolution: 1.6→42.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.59 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1043 5.3 %RANDOM
Rwork0.192 ---
obs-18801 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.25 Å2 / Biso mean: 32.8 Å2 / Biso min: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.6→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 0 71 1254
Biso mean---40.25 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191210
X-RAY DIFFRACTIONr_bond_other_d0.0020.021008
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9121636
X-RAY DIFFRACTIONr_angle_other_deg0.84832354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0555149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82125.94269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34315192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.918154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
X-RAY DIFFRACTIONr_rigid_bond_restr3.05331210
X-RAY DIFFRACTIONr_sphericity_bonded13.41751187
LS refinement shellResolution: 1.6→1.657 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.378 88 -
Rwork0.386 1847 -
all-1935 -
obs--99.95 %

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