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- PDB-3nz3: Crystal structure of the mucin-binding domain of Spr1345 from Str... -

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Basic information

Entry
Database: PDB / ID: 3nz3
TitleCrystal structure of the mucin-binding domain of Spr1345 from Streptococcus pneumoniae
ComponentsPutative uncharacterized protein
KeywordsCELL ADHESION / All beta sheets / Ig-like fold / Mucin-binding / Mucin / Cell surface
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Immunoglobulin-like - #4300 / Mub B2-like domain / Muc B2-like domain / 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
TRIETHYLENE GLYCOL / Gram-positive cocci surface proteins LPxTG domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsDu, Y. / He, Y.-X. / Zhang, Z.-Y. / Yang, Y.-H. / Shi, W.-W. / Frolet, C. / Guilmi, A.M. / Vernet, T. / Zhou, C.-Z. / Chen, Y.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structure of the mucin-binding domain of Spr1345 from Streptococcus pneumoniae
Authors: Du, Y. / He, Y.-X. / Zhang, Z.-Y. / Yang, Y.-H. / Shi, W.-W. / Frolet, C. / Guilmi, A.M. / Vernet, T. / Zhou, C.-Z. / Chen, Y.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9843
Polymers12,7381
Non-polymers2462
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.160, 73.160, 108.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

21A-106-

HOH

31A-113-

HOH

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Components

#1: Protein Putative uncharacterized protein / Spr1345 protein


Mass: 12738.092 Da / Num. of mol.: 1 / Fragment: Mucin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr1345 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Ril / References: UniProt: Q8CYK3
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 4000, 0.1M Tris-HCl, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→37.48 Å / Num. obs: 10342 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1467 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→25.78 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 498 RANDOM
Rwork0.213 --
obs-9837 -
Refinement stepCycle: LAST / Resolution: 2→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms793 0 15 150 958

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