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- PDB-4uto: Crystal structure of pneumococcal surface antigen PsaA D280N in t... -

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Basic information

Entry
Database: PDB / ID: 4uto
TitleCrystal structure of pneumococcal surface antigen PsaA D280N in the Cd-bound, open state
ComponentsMANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
KeywordsMETAL BINDING PROTEIN / ATP BINDING / CASSETTE TRANSPORTER
Function / homology
Function and homology information


metal ion transport / cell adhesion / metal ion binding / plasma membrane
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Manganese ABC transporter substrate-binding lipoprotein PsaA
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLuo, Z. / Counago, R.M. / Maher, M. / Kobe, B.
CitationJournal: Nat Commun / Year: 2015
Title: Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae.
Authors: Begg, S.L. / Eijkelkamp, B.A. / Luo, Z. / Counago, R.M. / Morey, J.R. / Maher, M.J. / Ong, C.L. / McEwan, A.G. / Kobe, B. / O'Mara, M.L. / Paton, J.C. / McDevitt, C.A.
History
DepositionJul 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 2.0Mar 28, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
B: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7466
Polymers69,2772
Non-polymers4694
Water9,188510
1
A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8733
Polymers34,6381
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8733
Polymers34,6381
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.737, 59.292, 62.468
Angle α, β, γ (deg.)106.86, 104.90, 93.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN / PNEUMOCOCCAL SURFACE ADHESIN A


Mass: 34638.285 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A4G2
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.59 % / Description: NONE
Crystal growpH: 8.7
Details: 12.5 % (W/V) PEG 1000, 12.5% (W/V) PEG 3350, 12.5% (V/V) MPD, 0.1 M TRIZMA-BICINE, PH 8.7 AND 0.01 M CDCL2

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→19.73 Å / Num. obs: 73161 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 11.35 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKA

3zka


Resolution: 1.55→19.73 Å / SU ML: 0.2 / σ(F): 1.96 / Phase error: 21.39
RfactorNum. reflection% reflection
Rfree0.214 -10 %
Rwork0.181 --
obs-73160 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.53 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 18 510 4962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064552
X-RAY DIFFRACTIONf_angle_d1.3316150
X-RAY DIFFRACTIONf_dihedral_angle_d13.4431738
X-RAY DIFFRACTIONf_chiral_restr0.059672
X-RAY DIFFRACTIONf_plane_restr0.008794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58880.29321380.28145002X-RAY DIFFRACTION95
1.5888-1.63170.33971440.26114959X-RAY DIFFRACTION95
1.6317-1.67970.28061380.2495031X-RAY DIFFRACTION96
1.6797-1.73390.26211420.22435073X-RAY DIFFRACTION95
1.7339-1.79580.23941480.20315030X-RAY DIFFRACTION96
1.7958-1.86760.23671500.19895071X-RAY DIFFRACTION97
1.8676-1.95260.20351440.1755056X-RAY DIFFRACTION97
1.9526-2.05540.19731460.16865093X-RAY DIFFRACTION97
2.0554-2.1840.17861440.16185132X-RAY DIFFRACTION97
2.184-2.35240.2091480.15765131X-RAY DIFFRACTION98
2.3524-2.58870.20341380.16275155X-RAY DIFFRACTION98
2.5887-2.96220.21281470.17075154X-RAY DIFFRACTION98
2.9622-3.72790.20981460.16185109X-RAY DIFFRACTION97
3.7279-19.73010.18471490.17745133X-RAY DIFFRACTION97

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