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- PDB-6y9u: Crystal structure of PnrA from S. pneumoniae in complex with adenosine -

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Basic information

Entry
Database: PDB / ID: 6y9u
TitleCrystal structure of PnrA from S. pneumoniae in complex with adenosine
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / Nucleoside substrate-binding protein
Function / homology
Function and homology information


: / ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE / NICKEL (II) ION / Lipoprotein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBatuecas, M.T. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-90030-P Spain
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-binding Protein PnrA.
Authors: Abdullah, M.R. / Batuecas, M.T. / Jennert, F. / Voss, F. / Westhoff, P. / Kohler, T.P. / Molina, R. / Hirschmann, S. / Lalk, M. / Hermoso, J.A. / Hammerschmidt, S.
History
DepositionMar 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Lipoprotein
B: Lipoprotein
C: Lipoprotein
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,21915
Polymers140,7394
Non-polymers1,48011
Water5,549308
1
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5694
Polymers35,1851
Non-polymers3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5113
Polymers35,1851
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6285
Polymers35,1851
Non-polymers4444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5113
Polymers35,1851
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.221, 304.958, 128.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-683-

HOH

21D-612-

HOH

31D-628-

HOH

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Components

#1: Protein
Lipoprotein


Mass: 35184.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_0845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UPF3
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 600, 0.2 M calcium acetate and 0.1 M sodium cacodylate (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.5→49.06 Å / Num. obs: 50919 / % possible obs: 99.88 % / Redundancy: 11.3 % / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 13.6
Reflection shellResolution: 2.5→2.56 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3737 / CC1/2: 0.74 / Rpim(I) all: 0.36

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQW

2fqw


Resolution: 2.5→49.06 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.23 --RANDOM
Rwork0.19 ---
obs-50919 99.88 %-
Displacement parametersBiso max: 139.29 Å2 / Biso mean: 56.9129 Å2 / Biso min: 20.58 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9910 0 86 308 10304

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