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- PDB-3zk7: CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA IN THE MET... -

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Basic information

Entry
Database: PDB / ID: 3zk7
TitleCRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA IN THE METAL-FREE, OPEN STATE
ComponentsMANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
KeywordsMETAL TRANSPORT / ATP-BINDING CASSETTE TRANSPORTERS / LIPOPROTEIN / MEMBRANE TRANSPORT PROTEIN
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: 1.69 Å
AuthorsCounago, R.M. / Ween, M.P. / Bajaj, M. / Zuegg, J. / Cooper, M.A. / McEwan, A.G. / Paton, J.C. / Kobe, B. / McDevitt, C.A.
Citation
Journal: Nat. Chem. Biol. / Year: 2014
Title: Imperfect coordination chemistry facilitates metal ion release in the Psa permease.
Authors: Counago, R.M. / Ween, M.P. / Begg, S.L. / Bajaj, M. / Zuegg, J. / O'Mara, M.L. / Cooper, M.A. / McEwan, A.G. / Paton, J.C. / Kobe, B. / McDevitt, C.A.
#1: Journal: Structure / Year: 1998
Title: The Crystal Structure of Pneumococcal Surface Antigen Psaa Reveals a Metal-Binding Site and a Novel Structure for a Putative Abc-Type Binding Protein.
Authors: Lawrence, M.C. / Pilling, P.A. / Epa, V.C. / Berry, A.M. / Ogunniyi, A.D. / Paton, J.C.
#2: Journal: Plos Pathog. / Year: 2011
Title: A Molecular Mechanism for Bacterial Susceptibility to Zinc.
Authors: McDevitt, C.A. / Ogunniyi, A.D. / Valkov, E. / Lawrence, M.C. / Kobe, B. / McEwan, A.G. / Paton, J.C.
History
DepositionJan 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Jan 8, 2014Group: Database references
Revision 2.0Mar 28, 2018Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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] / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Dec 20, 2023Group: 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 / 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 / _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)63,3796
Polymers62,8912
Non-polymers4894
Water12,016667
1
A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6903
Polymers31,4451
Non-polymers2442
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)31,6903
Polymers31,4451
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.940, 59.910, 62.630
Angle α, β, γ (deg.)107.02, 103.90, 96.96
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 / PSAA


Mass: 31445.387 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A4G2
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


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


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.16 Å3/Da / Density % sol: 42.96 % / Description: NONE
Crystal growTemperature: 293 K
Details: 12.5% W/V PEG 1,000 12.5% W/V PEG 3,350, 12.5% V/V MPD; 0.1 M TRIZMA/BICINE PH 8.7 AFTER 7-10 DAYS AT 293 K, FOLLOWING STREAK-SEEDING OF PRE-EQUILIBRATED (24 HOURS) DROPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369
DetectorType: ADSC CCD / Detector: CCD / Details: SILICON MIRRORS (ADAPTIVE AND U-BENT)
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.69→17 Å / Num. obs: 57796 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 24.88 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.7
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.6 / % possible all: 86.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSZ

1psz


Resolution: 1.69→17.04 Å / Cor.coef. Fo:Fc: 0.9626 / Cor.coef. Fo:Fc free: 0.9485 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 2930 5.07 %RANDOM
Rwork0.1613 ---
obs0.1629 57796 95.56 %-
Displacement parametersBiso mean: 28.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.7746 Å2-1.0726 Å20.1674 Å2
2--0.2982 Å2-0.4855 Å2
3---1.4765 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: LAST / Resolution: 1.69→17.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 32 667 5131
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019004HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0516380HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2570SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1226HARMONIC5
X-RAY DIFFRACTIONt_it9004HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.26
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion602SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9973SEMIHARMONIC4
LS refinement shellResolution: 1.69→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2241 208 5.11 %
Rwork0.2031 3861 -
all0.2041 4069 -
obs--95.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.505-0.0636-0.08662.23640.43250.7251-0.01390.0074-0.0652-0.0533-0.0240.00050.0716-0.00090.038-0.02250.02470.0299-0.0695-0.0246-0.05631.1117-18.327236.711
23.3971-0.6402-3.42721.5810.15033.4711-0.10070.078-0.10360.22120.05010.08150.1524-0.17490.0506-0.02580.01080.0177-0.0529-0.0277-0.0461-4.2923-3.150747.421
30.4953-0.0698-0.07152.4540.15060.5035-0.0665-0.128-0.00890.12870.0767-0.48250.05520.128-0.0101-0.02880.0455-0.03190.033-0.0420.073815.3198-7.88845.0847
40.7561-0.22170.5091.7698-0.40841.366-0.0927-0.06460.0504-0.11980.0498-0.0226-0.1612-0.06960.0429-0.03420.00350.0148-0.0596-0.0423-0.0469-0.72458.898434.9286
50.5648-0.1549-0.35962.45240.0571.06590.02880.02610.04260.0946-0.0717-0.0713-0.0908-0.00980.0429-0.0446-0.011-0.0226-0.0634-0.0246-0.03710.7988-5.228111.0108
60.95750.14182.04350.83110.62693.6013-0.0139-0.17150.0308-0.1462-0.14140.0556-0.0646-0.26890.1553-0.02070.0167-0.0219-0.0306-0.04110.0029-3.4783-20.38340.1873
70.2572-0.576-0.00354.19510.31570.8650.03210.12030.1208-0.244-0.0254-0.7581-0.05480.133-0.0067-0.107-0.00010.05390.02010.01580.114315.863-14.54262.6527
80.5454-0.08980.04272.856-0.12310.7845-0.00510.0102-0.03420.1276-0.01570.00810.0946-0.00330.0209-0.0620.012-0.0075-0.0567-0.0303-0.03631.0056-32.519212.3719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|32 - 123 }
2X-RAY DIFFRACTION2{ A|124 - 145 }
3X-RAY DIFFRACTION3{ A|146 - 196 }
4X-RAY DIFFRACTION4{ A|197 - 309 }
5X-RAY DIFFRACTION5{ B|32 - 123 }
6X-RAY DIFFRACTION6{ B|124 - 145 }
7X-RAY DIFFRACTION7{ B|146 - 196 }
8X-RAY DIFFRACTION8{ B|197 - 309 }

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