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- PDB-9gn3: The 3D structure of MsrR from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 9gn3
TitleThe 3D structure of MsrR from Streptococcus pneumoniae
ComponentsRegulatory protein MsrR
KeywordsSTRUCTURAL PROTEIN / S.pneumoniae / LCP / Psr / cell wall teichoic acid / capsular polysaccharide / protein dynamics
Function / homology: / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / plasma membrane / Regulatory protein MsrR
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMoche, M. / Sala, B.M. / Sandalova, T. / Achour, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-05798_VR Sweden
CitationJournal: Crystals / Year: 2024
Title: Crystallographic and NMR Study of Streptococcus pneumonia LCP Protein PsrSp Indicate the Importance of Dynamics in Four Long Loops for Ligand Specificity
Authors: Sandalova, T. / Sala, B.M. / Moche, M. / Ljunggren, H.G. / Alici, E. / Henriques-Normark, B. / Agback, T. / Lesovoy, D. / Agback, P. / Achour, A.
History
DepositionAug 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein MsrR
B: Regulatory protein MsrR
C: Regulatory protein MsrR


Theoretical massNumber of molelcules
Total (without water)102,1563
Polymers102,1563
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Each protein chain in the asymmetric unit forms a stable trimer around the 3-fold axis of the P3 2 1 space group, according to PISA server...
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-7 kcal/mol
Surface area38920 Å2
Unit cell
Length a, b, c (Å)130.631, 130.631, 100.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21B-574-

HOH

31C-565-

HOH

41C-569-

HOH

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Components

#1: Protein Regulatory protein MsrR


Mass: 34052.141 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Construct has a C-terminal HisTag / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: spr1226 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DPD6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 25mM NaPhosphate pH 6.8 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976323 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976323 Å / Relative weight: 1
ReflectionResolution: 2.15→46 Å / Num. obs: 34775 / % possible obs: 64.2 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.12 / Net I/σ(I): 13.7
Reflection shellResolution: 2.15→2.304 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1738 / CC1/2: 0.595 / Rpim(I) all: 0.482 / Rrim(I) all: 1.202 / % possible all: 17.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
STARANISOdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 17.244 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.657 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25905 1710 4.9 %RANDOM
Rwork0.20387 ---
obs0.20659 33065 64.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.15→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 0 226 7082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127028
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166724
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.8179513
X-RAY DIFFRACTIONr_angle_other_deg0.5141.77115437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.621537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.135101241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021609
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7413.2693591
X-RAY DIFFRACTIONr_mcbond_other2.743.2693591
X-RAY DIFFRACTIONr_mcangle_it4.3185.8584494
X-RAY DIFFRACTIONr_mcangle_other4.3185.8594495
X-RAY DIFFRACTIONr_scbond_it3.2543.5323437
X-RAY DIFFRACTIONr_scbond_other3.2533.5323438
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2366.3775020
X-RAY DIFFRACTIONr_long_range_B_refined9.1113931644
X-RAY DIFFRACTIONr_long_range_B_other9.10738.9931610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 16 -
Rwork0.326 284 -
obs--7.56 %
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)
13.61210.5205-1.59871.84320.6292.46630.10880.03350.27870.0019-0.02120.3402-0.2235-0.208-0.08760.0613-0.01030.01360.07980.01550.141246.958630.738-4.7508
23.70641.9908-1.57733.8869-1.78281.9042-0.34790.90.1594-0.25060.34660.1027-0.0386-0.27680.00130.0885-0.119-0.04380.3636-0.02950.229538.929425.3479-24.8586
33.38810.6889-1.47350.9092-0.37781.5069-0.06380.0866-0.2266-0.00850.0201-0.04060.1402-0.05630.04380.0959-0.0395-0.04120.0725-0.0220.18748.332822.4157-9.0483
43.12140.7913-0.23352.9265-1.56312.67010.02610.04570.40520.13210.04180.0947-0.2315-0.0165-0.0680.0376-0.00910.01240.07480.00020.12315.602312.217719.5189
55.48390.6228-1.29651.12760.19252.24610.1453-0.60430.20990.2056-0.15260.16660.0311-0.16550.00730.0891-0.0815-0.02210.1711-0.01660.24424.247215.253339.6213
63.06931.236-1.56351.6377-1.01771.4712-0.0471-0.1604-0.29130.0224-0.1094-0.21560.10180.17280.15650.02530.0002-0.02090.083-0.01630.182222.66426.626822.9616
71.7782-0.3349-0.72823.1905-0.62932.0267-0.0701-0.0644-0.25190.0460.15130.42880.1605-0.2003-0.08120.0603-0.003-0.02040.03980.02260.223461.089517.910538.8252
82.6473-0.18750.64483.76050.24550.7786-0.05590.07840.0579-0.4880.1060.1129-0.0945-0.054-0.050.235-0.0326-0.04870.0298-0.02560.229660.27078.63718.6889
90.8298-0.11540.00722.8626-0.95181.3225-0.03-0.0151-0.0975-0.17020.0505-0.08460.14640.0853-0.02050.05670.0255-0.0340.0226-0.00850.239368.445914.976334.1454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A130 - 245
2X-RAY DIFFRACTION2A246 - 353
3X-RAY DIFFRACTION3A354 - 428
4X-RAY DIFFRACTION4B130 - 244
5X-RAY DIFFRACTION5B245 - 356
6X-RAY DIFFRACTION6B357 - 427
7X-RAY DIFFRACTION7C130 - 245
8X-RAY DIFFRACTION8C246 - 353
9X-RAY DIFFRACTION9C354 - 427

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