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- PDB-3zgh: Crystal structure of the KRT10-binding region domain of the pneum... -

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Basic information

Entry
Database: PDB / ID: 3zgh
TitleCrystal structure of the KRT10-binding region domain of the pneumococcal serine rich repeat protein PsrP
ComponentsCELL WALL SURFACE ANCHOR FAMILY PROTEIN
KeywordsSTRUCTURAL PROTEIN / MSCRAMM / KERATIN-10
Function / homology
Function and homology information


Gram-positive-bacterium-type cell wall / symbiont-mediated perturbation of host defense response / single-species biofilm formation / cell adhesion / cell surface / DNA binding / extracellular region
Similarity search - Function
Immunoglobulin-like - #3400 / Serine-rich repeat adhesion glycoprotein / 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
ACETATE ION / Pneumococcal serine-rich repeat protein / Pneumococcal serine-rich repeat protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchulte, T. / Loefling, J. / Mikaelsson, C. / Kikhney, A. / Hentrich, K. / Diamante, A. / Ebel, C. / Normark, S. / Svergun, D. / Henriques-Normark, B. / Achour, A.
CitationJournal: Open Biol / Year: 2014
Title: The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold.
Authors: Tim Schulte / Jonas Löfling / Cecilia Mikaelsson / Alexey Kikhney / Karina Hentrich / Aurora Diamante / Christine Ebel / Staffan Normark / Dmitri Svergun / Birgitta Henriques-Normark / Adnane Achour /
Abstract: Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human ...Streptococcus pneumoniae is a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187-385) determined to 2.0 Å resolution. BR187-385 adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.
History
DepositionDec 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 1, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5637
Polymers22,1391
Non-polymers4236
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.510, 74.510, 121.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

21A-2096-

HOH

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Components

#1: Protein CELL WALL SURFACE ANCHOR FAMILY PROTEIN / PNEUMOCOCCAL SERINE RICH REPEAT PROTEIN / SRRP


Mass: 22139.418 Da / Num. of mol.: 1 / Fragment: KRT10-BINDING REGION DOMAIN, RESIDUES 187-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q97P71, UniProt: A0A0H2URK1*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.9 Å3/Da / Density % sol: 35.35 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: WELL-DIFFRACTING CRYSTALS OF WILD-TYPE AND SE-MET-BR187-385 WERE OBTAINED IN 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 25% PEG4000 (W/V) USING THE SITTING DROP VAPOR- ...Details: WELL-DIFFRACTING CRYSTALS OF WILD-TYPE AND SE-MET-BR187-385 WERE OBTAINED IN 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 25% PEG4000 (W/V) USING THE SITTING DROP VAPOR-DIFFUSION METHOD FOLLOWED BY MICRO-SEEDING.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2→48.3 Å / Num. obs: 44053 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Biso Wilson estimate: 35.34 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL OBTAINED FROM SAD EXPERIMENT

Resolution: 2→48.318 Å / SU ML: 0.61 / σ(F): 1.31 / Phase error: 16.43 / Stereochemistry target values: ML
Details: A SINGLE RAMACHANDRAN PLOT OUTLIER WAS FOUND IN THE FINAL MODEL CORRESPONDING TO RESIDUE T271, LOCATED IN A LOOP REGION WITH WEAK ELECTRON DENSITY. RESIDUES T311, Q312 AND G313 ARE LOCALIZED ...Details: A SINGLE RAMACHANDRAN PLOT OUTLIER WAS FOUND IN THE FINAL MODEL CORRESPONDING TO RESIDUE T271, LOCATED IN A LOOP REGION WITH WEAK ELECTRON DENSITY. RESIDUES T311, Q312 AND G313 ARE LOCALIZED AT THE BEGINNING OF A TURN MOTIF WHICH WAS DIFFICULT TO MODEL. RESIDUES S376 AND S377 ARE LOCALIZED AT THE C-TERMINUS OF THE PROTEIN WITH WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.201 2176 4.9 %
Rwork0.1769 --
obs0.1781 44052 99.95 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.984 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 42.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→48.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 28 114 1494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121403
X-RAY DIFFRACTIONf_angle_d1.4171896
X-RAY DIFFRACTIONf_dihedral_angle_d13.242494
X-RAY DIFFRACTIONf_chiral_restr0.09211
X-RAY DIFFRACTIONf_plane_restr0.006239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.04340.28961330.26042593X-RAY DIFFRACTION100
2.0434-2.09090.21421340.24082642X-RAY DIFFRACTION100
2.0909-2.14320.19211390.20742611X-RAY DIFFRACTION100
2.1432-2.20120.20911360.18322639X-RAY DIFFRACTION100
2.2012-2.26590.20041310.17412619X-RAY DIFFRACTION100
2.2659-2.33910.19631410.16752625X-RAY DIFFRACTION100
2.3391-2.42270.22241380.17492581X-RAY DIFFRACTION100
2.4227-2.51970.19481370.16732613X-RAY DIFFRACTION100
2.5197-2.63430.1961400.17772630X-RAY DIFFRACTION100
2.6343-2.77320.18711360.15752621X-RAY DIFFRACTION100
2.7732-2.94690.18981370.16492608X-RAY DIFFRACTION100
2.9469-3.17440.20261420.17462608X-RAY DIFFRACTION100
3.1744-3.49380.1891350.17592628X-RAY DIFFRACTION100
3.4938-3.99920.17171320.1672605X-RAY DIFFRACTION100
3.9992-5.03770.17961330.14422622X-RAY DIFFRACTION100
5.0377-48.3320.26031320.21742631X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.895 Å / Origin y: -34.4247 Å / Origin z: -4.5657 Å
111213212223313233
T0.1409 Å20.0471 Å2-0.0278 Å2-0.2274 Å20.0212 Å2--0.2305 Å2
L2.6323 °20.4247 °21.354 °2-1.7884 °21.0174 °2--4.1183 °2
S0.105 Å °-0.1908 Å °-0.1624 Å °0.0519 Å °0.0793 Å °-0.0784 Å °0.3283 Å °0.4245 Å °-0.1281 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESID 203:379)

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