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- PDB-7jjb: Crystal structure of Zn(II)-bound ZinT-like domain of Streptococc... -

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Basic information

Entry
Database: PDB / ID: 7jjb
TitleCrystal structure of Zn(II)-bound ZinT-like domain of Streptococcus pneumoniae AdcA
ComponentsZinc-binding lipoprotein AdcA
KeywordsMETAL BINDING PROTEIN / AdcA / ZinT / SBP / ATP-binding cassette transporter / Zn acquisition
Function / homology
Function and homology information


zinc ion transport / establishment of competence for transformation / cell adhesion / zinc ion binding / plasma membrane
Similarity search - Function
ZinT domain / ZinT (YodA) periplasmic lipocalin-like zinc-recruitment / Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Calycin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Zinc-binding lipoprotein AdcA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLuo, Z. / More, J.R. / Kobe, B. / McDevitt, C.A.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1080784 Australia
National Health and Medical Research Council (NHMRC, Australia)1122582 Australia
Australian Research Council (ARC)DP170102102 Australia
CitationJournal: Mbio / Year: 2021
Title: A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA.
Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / ...Authors: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / Kobe, B. / McDevitt, C.A.
History
DepositionJul 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: 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: Zinc-binding lipoprotein AdcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,19910
Polymers20,9061
Non-polymers2939
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.251, 50.091, 87.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-208-

NA

21A-457-

HOH

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Components

#1: Protein Zinc-binding lipoprotein AdcA


Mass: 20906.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: adcA, spr1975 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CWN2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 30 % (w/v) PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.1→19.72 Å / Num. obs: 79405 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 9.30931181088 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.2
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 7855 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OEK

1oek


Resolution: 1.1→19.72 Å / SU ML: 0.0905886820257 / Cross valid method: FREE R-VALUE / σ(F): 1.33414552556 / Phase error: 14.4594981077
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.167280499897 3917 4.93300085638 %
Rwork0.146947165944 75487 -
obs0.147950940525 79404 99.9949627242 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.3663010563 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 9 351 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006514023028531559
X-RAY DIFFRACTIONf_angle_d0.8962248212572115
X-RAY DIFFRACTIONf_chiral_restr0.0732753374994213
X-RAY DIFFRACTIONf_plane_restr0.00625984275128278
X-RAY DIFFRACTIONf_dihedral_angle_d15.9927611443564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11340.2339527411341370.2159976891832670X-RAY DIFFRACTION100
1.1134-1.12750.2241133211311580.202318541682636X-RAY DIFFRACTION100
1.1275-1.14230.191985051261470.197243586292646X-RAY DIFFRACTION100
1.1423-1.1580.2192502291961410.1880430689852657X-RAY DIFFRACTION100
1.158-1.17450.2004876597761450.18071988812657X-RAY DIFFRACTION100
1.1745-1.19210.192517330461400.1684585504962685X-RAY DIFFRACTION100
1.1921-1.21070.2083299819921430.1726418616762646X-RAY DIFFRACTION100
1.2107-1.23050.1750481560851360.1673404064942670X-RAY DIFFRACTION100
1.2305-1.25170.1730464627761630.1611240630212645X-RAY DIFFRACTION100
1.2517-1.27450.1699460995981180.1551827849722678X-RAY DIFFRACTION100
1.2745-1.2990.1882987537691280.1585047984282677X-RAY DIFFRACTION100
1.299-1.32550.1711172180581240.1495114752422706X-RAY DIFFRACTION100
1.3255-1.35430.1822693330881270.1483796392022699X-RAY DIFFRACTION100
1.3543-1.38580.1840214256681300.1454231439632681X-RAY DIFFRACTION100
1.3858-1.42050.1795214792441370.1445546842652676X-RAY DIFFRACTION100
1.4205-1.45890.1449035967971460.1356655701382674X-RAY DIFFRACTION100
1.4589-1.50180.1513945090051400.1289012420442672X-RAY DIFFRACTION100
1.5018-1.55020.1563720849261610.1296247757532673X-RAY DIFFRACTION100
1.5502-1.60560.1270072929381400.1219728837642685X-RAY DIFFRACTION100
1.6056-1.66990.1434878977871360.1223634693472704X-RAY DIFFRACTION100
1.6699-1.74580.1709110848531380.1330884984562708X-RAY DIFFRACTION100
1.7458-1.83780.1393238184781430.1327725057422701X-RAY DIFFRACTION100
1.8378-1.95290.1723840106261300.1398359475392722X-RAY DIFFRACTION100
1.9529-2.10350.1660826438091490.1414696716812719X-RAY DIFFRACTION100
2.1035-2.31490.1493255701411330.144231594432732X-RAY DIFFRACTION100
2.3149-2.64920.1672355237321350.1485789450642769X-RAY DIFFRACTION100
2.6492-3.33510.1783516831961450.1480364168562791X-RAY DIFFRACTION100
3.33-19.720.1585652072371470.1448114089472908X-RAY DIFFRACTION99.8692383132

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