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- PDB-4nsm: crystal structure of the streptococcal collagen-like protein 2 gl... -

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Basic information

Entry
Database: PDB / ID: 4nsm
Titlecrystal structure of the streptococcal collagen-like protein 2 globular domain from invasive M3-type group A Streptococcus
ComponentsCollagen-like protein SclB
KeywordsSTRUCTURAL PROTEIN / six-helix bundle
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2770 / : / M protein-type anchor domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / LPXTG cell wall anchor motif / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Collagen-like protein SclB / Collagen-like protein SclB
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsBerisio, R. / Squeglia, F. / Lukomski, S. / Bachert, B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Crystal Structure of the Streptococcal Collagen-like Protein 2 Globular Domain from Invasive M3-type Group A Streptococcus Shows Significant Similarity to Immunomodulatory HIV Protein gp41.
Authors: Squeglia, F. / Bachert, B. / De Simone, A. / Lukomski, S. / Berisio, R.
History
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen-like protein SclB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4334
Polymers10,1191
Non-polymers3143
Water1,76598
1
A: Collagen-like protein SclB
hetero molecules

A: Collagen-like protein SclB
hetero molecules

A: Collagen-like protein SclB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,30012
Polymers30,3583
Non-polymers9439
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7030 Å2
ΔGint-93 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.405, 44.405, 227.767
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-602-

TRS

21A-602-

TRS

31A-709-

HOH

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Components

#1: Protein Collagen-like protein SclB


Mass: 10119.227 Da / Num. of mol.: 1 / Fragment: V domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: ATCC BAA-595 / MGAS315 / Gene: sclB, SpyM3_0738 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K7M7, UniProt: A0A0H2UUG0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 0.05M Ammonium sulfate, 0.05M BIS-TRIS pH 6.5, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH), EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 12, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. all: 13802 / Num. obs: 13802 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.52→1.55 Å / Rmerge(I) obs: 0.345 / % possible all: 86.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→14.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.632 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.23995 822 6.9 %RANDOM
Rwork0.19546 ---
obs0.19854 11101 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.793 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms580 0 18 98 696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022622
X-RAY DIFFRACTIONr_bond_other_d0.0040.02441
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.999839
X-RAY DIFFRACTIONr_angle_other_deg1.06931073
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 58 -
Rwork0.194 804 -
obs--100 %

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