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- PDB-4rmb: Crystal structure of keratin 4 binding domain of surface adhesin ... -

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Basic information

Entry
Database: PDB / ID: 4rmb
TitleCrystal structure of keratin 4 binding domain of surface adhesin Srr-1 of S.agalactiae
ComponentsSerine rich repeat protein-1 (Srr-1)
KeywordsCELL ADHESION / Variant of DEv-IgG fold / adhesin / keratin 4 / bacterial cell surface / beta sheet complementation
Function / homology
Function and homology information


keratin filament binding / symbiont entry into host / cell adhesion / cell surface / extracellular region / metal ion binding
Similarity search - Function
Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Serine-rich repeat adhesion glycoprotein / Immunoglobulin-like - #1290 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Adhesion domain superfamily ...Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / Serine-rich repeat adhesion glycoprotein / Immunoglobulin-like - #1290 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Adhesion domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae NEM316 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPonnuraj, K. / Sundaresan, R.
CitationJournal: Int.J.Biol.Macromol. / Year: 2015
Title: Structure of KRT4 binding domain of Srr-1 from Streptococcus agalactiae reveals a novel beta-sheet complementation.
Authors: Sundaresan, R. / Samen, U. / Ponnuraj, K.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Serine rich repeat protein-1 (Srr-1)
B: Serine rich repeat protein-1 (Srr-1)


Theoretical massNumber of molelcules
Total (without water)37,0532
Polymers37,0532
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-28 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.050, 71.890, 47.320
Angle α, β, γ (deg.)90.00, 96.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine rich repeat protein-1 (Srr-1)


Mass: 18526.262 Da / Num. of mol.: 2 / Fragment: Keratin 4 binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae NEM316 (bacteria)
Strain: NEM316 / Gene: gbs1529 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8E473
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.78 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 25% (w/v) PEG 3350 (Sigma), 100 mM Lithium chloride and 100 mM Imidazole, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.7→35.95 Å / Num. all: 27350 / Num. obs: 27350 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.66 / Num. unique all: 27350 / % possible all: 80.7

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Processing

Software
NameVersionClassification
Auto-Rickshawphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MBO

4mbo


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 797 -RANDOM
Rwork0.2215 ---
all-28630 --
obs-27224 95.1 %-
Displacement parametersBiso mean: 24.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-3.306 Å2
2---4.579 Å20 Å2
3---4.009 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 0 107 2402

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