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- PDB-6yag: Crystal structure of PnrA from S. pneumoniae in complex with thymidine -

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Basic information

Entry
Database: PDB / ID: 6yag
TitleCrystal structure of PnrA from S. pneumoniae in complex with thymidine
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 / NICKEL (II) ION / THYMIDINE / Lipoprotein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)141,43316
Polymers139,9944
Non-polymers1,43912
Water4,576254
1
C: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2993
Polymers34,9981
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2993
Polymers34,9981
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3584
Polymers34,9981
Non-polymers3603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4766
Polymers34,9981
Non-polymers4775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.966, 303.818, 128.417
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-505-

HOH

21B-560-

HOH

31B-572-

HOH

41B-573-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13C
23D
14A
24B
15A
25D
16B
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROCA4 - 3312 - 329
21SERSERPROPROAB4 - 3312 - 329
12SERSERPROPROCA4 - 3312 - 329
22SERSERPROPROBC4 - 3312 - 329
13HISHISPROPROCA5 - 3313 - 329
23HISHISPROPRODD5 - 3313 - 329
14SERSERGLUGLUAB4 - 3322 - 330
24SERSERGLUGLUBC4 - 3322 - 330
15HISHISPROPROAB5 - 3313 - 329
25HISHISPROPRODD5 - 3313 - 329
16HISHISPROPROBC5 - 3313 - 329
26HISHISPROPRODD5 - 3313 - 329

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Lipoprotein


Mass: 34998.469 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.: 7 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2O5
#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.: 254 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
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: 0.979336 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979336 Å / Relative weight: 1
ReflectionResolution: 2.55→49.21 Å / Num. obs: 50223 / % possible obs: 99.2 % / Redundancy: 7.2 % / CC1/2: 0.96 / Rpim(I) all: 0.16 / Net I/σ(I): 5.1
Reflection shellResolution: 2.55→2.63 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4624 / CC1/2: 0.52 / Rpim(I) all: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQW

2fqw


Resolution: 2.55→49.21 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.4 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.667 / ESU R Free: 0.308
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2579 5.1 %RANDOM
Rwork0.2085 ---
obs0.2108 47620 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.13 Å2 / Biso mean: 47.42 Å2 / Biso min: 11.41 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å20 Å2
2---0.28 Å20 Å2
3----1.96 Å2
Refinement stepCycle: final / Resolution: 2.55→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9852 0 79 254 10185
Biso mean--37.26 35.23 -
Num. residues----1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310125
X-RAY DIFFRACTIONr_bond_other_d0.0020.0189103
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.62713689
X-RAY DIFFRACTIONr_angle_other_deg1.2631.58721208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83951324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26625.537484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.242151646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3371518
X-RAY DIFFRACTIONr_chiral_restr0.0610.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021992
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C99760.08
12A99760.08
21C99560.08
22B99560.08
31C99770.08
32D99770.08
41A99950.07
42B99950.07
51A99370.07
52D99370.07
61B100300.06
62D100300.06
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 191 -
Rwork0.316 3503 -
all-3694 -
obs--99.68 %

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