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- PDB-6ya4: Crystal structure of PnrA from S. pneumoniae in complex with cytidine -

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Basic information

Entry
Database: PDB / ID: 6ya4
TitleCrystal structure of PnrA from S. pneumoniae in complex with cytidine
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 / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Lipoprotein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 11, 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

Downloads & links

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Assembly

Deposited unit
C: Lipoprotein
A: Lipoprotein
B: Lipoprotein
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,39418
Polymers140,7394
Non-polymers1,65514
Water8,989499
1
C: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6045
Polymers35,1851
Non-polymers4204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6515
Polymers35,1851
Non-polymers4674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5934
Polymers35,1851
Non-polymers4083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5454
Polymers35,1851
Non-polymers3613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.612, 304.386, 128.383
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
11B-577-

HOH

21B-622-

HOH

31D-528-

HOH

41D-548-

HOH

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Components

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Protein , 1 types, 4 molecules CABD

#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

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Non-polymers , 5 types, 513 molecules

#2: Chemical
ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N3O5
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
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: 2.2→49.12 Å / Num. obs: 78306 / % possible obs: 99.7 % / Redundancy: 7.7 % / CC1/2: 0.99 / Rpim(I) all: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4445 / CC1/2: 0.71 / Rpim(I) all: 0.62

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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: 2.2→49.07 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.24 --RANDOM
Rwork0.2 ---
obs-78306 99.7 %-
Displacement parametersBiso max: 135.43 Å2 / Biso mean: 44.8793 Å2 / Biso min: 13.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9908 0 93 499 10500

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