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- PDB-6lnw: Crystal structure of accessory secretory protein 1,2 and 3 in Str... -

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Basic information

Entry
Database: PDB / ID: 6lnw
TitleCrystal structure of accessory secretory protein 1,2 and 3 in Streptococcus pneumoniae
Components
  • Accessory secretory protein Asp1
  • Accessory secretory protein Asp2
  • Accessory secretory protein Asp3
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


Accessory Sec system protein Asp2 / Accessory Sec system GspB-transporter / Accessory Sec system protein Asp3 / Accessory Sec secretory system ASP3 / Accessory secretory system protein Asp1 / Accessory Sec system protein Asp1
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Conserved domain protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGuo, C. / Feng, Z. / Zuo, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770787 China
National Natural Science Foundation of China (NSFC)31670732 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural and functional insights into the Asp1/2/3 complex mediated secretion of pneumococcal serine-rich repeat protein PsrP.
Authors: Guo, C. / Feng, Z. / Zuo, G. / Jiang, Y.L. / Zhou, C.Z. / Chen, Y. / Hou, W.T.
History
DepositionJan 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Accessory secretory protein Asp1
B: Accessory secretory protein Asp2
C: Accessory secretory protein Asp3


Theoretical massNumber of molelcules
Total (without water)139,2533
Polymers139,2533
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-18 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.158, 101.158, 196.851
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Accessory secretory protein Asp1


Mass: 62189.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: TIGR4 / Gene: SP_1762 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UR88
#2: Protein Accessory secretory protein Asp2


Mass: 58828.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: TIGR4 / Gene: SP_1761 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2URA6
#3: Protein Accessory secretory protein Asp3


Mass: 18235.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: TIGR4 / Gene: SP_1760 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2URJ0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.0, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26531 / % possible obs: 99.85 % / Redundancy: 4.7 % / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 12.25
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 2586 / CC1/2: 0.833 / CC star: 0.953

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vae

5vae


Resolution: 2.9→42.94 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.2235 / WRfactor Rwork: 0.187 / FOM work R set: 0.8202 / SU Rfree: 0.3623 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 1310 4.9 %RANDOM
Rwork0.1971 ---
obs0.1993 25180 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.02 Å2 / Biso mean: 32.37 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 2.9→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6407 0 0 90 6497
Biso mean---25.28 -
Num. residues----767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196575
X-RAY DIFFRACTIONr_bond_other_d00.025895
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9418900
X-RAY DIFFRACTIONr_angle_other_deg3.561313675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8025763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20424.234359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.997151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0751536
X-RAY DIFFRACTIONr_chiral_restr0.0480.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027301
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021455
LS refinement shellResolution: 2.901→2.976 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 94 -
Rwork0.271 1822 -
all-1916 -
obs--99.74 %

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