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- PDB-6yab: Crystal structure of PnrA from S. pneumoniae in complex with uridine -

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Basic information

Entry
Database: PDB / ID: 6yab
TitleCrystal structure of PnrA from S. pneumoniae in complex with uridine
Components(Lipoprotein) x 3
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 / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / NICKEL (II) ION / URIDINE / Lipoprotein
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
CCC: Lipoprotein
AAA: Lipoprotein
BBB: Lipoprotein
DDD: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,96720
Polymers140,2074
Non-polymers1,76016
Water5,278293
1
CCC: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6265
Polymers35,1281
Non-polymers4994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1982
Polymers34,9531
Non-polymers2441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
BBB: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6667
Polymers35,1281
Non-polymers5386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4776
Polymers34,9981
Non-polymers4795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.021, 304.312, 128.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11BBB-543-

HOH

21BBB-587-

HOH

31DDD-507-

HOH

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Components

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Protein , 3 types, 4 molecules CCCBBBAAADDD

#1: Protein Lipoprotein


Mass: 35127.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Gene: SP_0845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UPF3
#2: Protein Lipoprotein


Mass: 34953.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Gene: SP_0845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UPF3
#3: Protein Lipoprotein


Mass: 34998.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Gene: SP_0845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UPF3

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Non-polymers , 5 types, 309 molecules

#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.86 %
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: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.3→49.135 Å / Num. obs: 68314 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.99 / Rpim(I) all: 0.03 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.35 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4545 / CC1/2: 0.93 / Rpim(I) all: 0.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQW

2fqw


Resolution: 2.3→49.09 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 --
Rwork0.21 --
obs-68314 100 %
Refinement stepCycle: LAST / Resolution: 2.3→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9879 0 90 294 10263

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