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

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Basic information

Entry
Database: PDB / ID: 3zgi
TitleCrystal structure of the KRT10-binding region domain of the pneumococcal serine rich repeat protein PsrP
ComponentsCELL WALL SURFACE ANCHOR FAMILY PROTEIN
KeywordsSTRUCTURAL PROTEIN / ADHESIN / KERATIN-10 / SRRP
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
Pneumococcal serine-rich repeat protein / Pneumococcal serine-rich repeat protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 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 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_struct_special_symmetry / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
C: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61910
Polymers66,9813
Non-polymers6387
Water2,630146
1
A: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5193
Polymers22,3271
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5814
Polymers22,3271
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5193
Polymers22,3271
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.580, 105.580, 120.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1379-

SO4

21A-2001-

HOH

31B-2031-

HOH

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Components

#1: Protein CELL WALL SURFACE ANCHOR FAMILY PROTEIN


Mass: 22326.998 Da / Num. of mol.: 3 / Fragment: KRT10-BINDING REGION DOMAIN, RESIDUES 188-386
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.41 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: 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: 0.97932
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.25→48.35 Å / Num. obs: 61680 / % possible obs: 100 % / Observed criterion σ(I): 3.2 / Redundancy: 4.6 % / Biso Wilson estimate: 36.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.18 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.25→48.35 Å / SU ML: 0.22 / σ(F): 1.31 / Phase error: 21.32 / Stereochemistry target values: ML
Details: NCS AND REFERENCE MODEL TORSION RESTRAINT WERE APPLIED TO CHAINS B/C AND CHAIN A, RESPECTIVELY. CRYSTAL PACKING ANALYSIS REVEALED THAT THE OVERALL MOBILITY OF CHAIN A WAS RELATIVELY HIGHER ...Details: NCS AND REFERENCE MODEL TORSION RESTRAINT WERE APPLIED TO CHAINS B/C AND CHAIN A, RESPECTIVELY. CRYSTAL PACKING ANALYSIS REVEALED THAT THE OVERALL MOBILITY OF CHAIN A WAS RELATIVELY HIGHER COMPARED TO THE MOBILITY OF CHAINS B AND C, AS REFLECTED BY HIGHER OVERALL B-FACTOR VALUES AND LOWER MAP CORRELATION COEFFICIENTS.
RfactorNum. reflection% reflection
Rfree0.2145 3090 5 %
Rwork0.186 --
obs0.1874 61669 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 34 146 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014105
X-RAY DIFFRACTIONf_angle_d1.475573
X-RAY DIFFRACTIONf_dihedral_angle_d13.91446
X-RAY DIFFRACTIONf_chiral_restr0.077618
X-RAY DIFFRACTIONf_plane_restr0.009698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.28520.2821430.22982672X-RAY DIFFRACTION100
2.2852-2.32260.25071420.22072656X-RAY DIFFRACTION100
2.3226-2.36270.22721380.21892655X-RAY DIFFRACTION100
2.3627-2.40560.25051430.21122680X-RAY DIFFRACTION100
2.4056-2.45190.2551370.21612658X-RAY DIFFRACTION100
2.4519-2.5020.23851400.21572660X-RAY DIFFRACTION100
2.502-2.55640.26161410.20382669X-RAY DIFFRACTION100
2.5564-2.61580.20121410.20632658X-RAY DIFFRACTION100
2.6158-2.68120.24211380.19532676X-RAY DIFFRACTION100
2.6812-2.75370.2221380.19792654X-RAY DIFFRACTION100
2.7537-2.83470.23471430.1962662X-RAY DIFFRACTION100
2.8347-2.92620.23531370.20142671X-RAY DIFFRACTION100
2.9262-3.03080.21661370.18942663X-RAY DIFFRACTION100
3.0308-3.15210.25211360.19032681X-RAY DIFFRACTION100
3.1521-3.29560.21741410.19312648X-RAY DIFFRACTION100
3.2956-3.46930.21791400.17512671X-RAY DIFFRACTION100
3.4693-3.68650.18061420.16352663X-RAY DIFFRACTION100
3.6865-3.97110.1871430.17732640X-RAY DIFFRACTION100
3.9711-4.37050.19561370.14952680X-RAY DIFFRACTION100
4.3705-5.00230.18291440.13712668X-RAY DIFFRACTION100
5.0023-6.30020.1791430.18542642X-RAY DIFFRACTION100
6.3002-48.36140.251460.24032652X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9521-0.4428-1.18937.6897-0.90566.2635-0.1593-0.4222-0.54740.5145-0.0253-0.06090.92710.41180.16040.65580.01150.06010.5589-0.01850.537444.178747.133418.8171
22.2648-0.53821.64031.359-0.70433.75530.0497-0.1495-0.23810.03990.10440.03170.56190.1187-0.1140.27280.0610.00090.18760.00830.27718.178640.168955.9002
32.13750.5887-1.88741.4096-1.04195.43110.11730.02320.18150.02620.07680.0869-0.59480.2128-0.13640.2136-0.03970.01640.1506-0.01450.234717.118466.30634.6647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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