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- PDB-3zka: CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN T... -

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Basic information

Entry
Database: PDB / ID: 3zka
TitleCRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA D280N IN THE METAL-BOUND, OPEN STATE
ComponentsMANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
KeywordsMETAL TRANSPORT / ATP-BINDING CASSETTE TRANSPORTERS / BACTERIAL ADHESION / CARRIER PROTEINS / LIPOPROTEINS / MEMBRANE TRANSPORT PROTEINS
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
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 ...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.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 / 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)63,2436
Polymers62,8892
Non-polymers3544
Water9,782543
1
A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6213
Polymers31,4441
Non-polymers1772
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)31,6213
Polymers31,4441
Non-polymers1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.524, 58.960, 62.130
Angle α, β, γ (deg.)106.18, 104.49, 94.39
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.028, -0.005), (0.027, -0.999, -0.025), (-0.006, 0.025, -1)
Vector: 0.854, -23.521, 47.389)

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Components

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


Mass: 31444.402 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-309 / Mutation: YES
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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.: 543 / 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: 2.21 Å3/Da / Density % sol: 44.31 % / 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: 1.55→22.7 Å / Num. obs: 71639 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 22.39 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 86.8

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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: 1.55→22.69 Å / Cor.coef. Fo:Fc: 0.9631 / Cor.coef. Fo:Fc free: 0.9527 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.082
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9429. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9429. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 3615 5.05 %RANDOM
Rwork0.1652 ---
obs0.1669 71639 95.86 %-
Displacement parametersBiso mean: 28.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.5974 Å2-0.2239 Å2-0.1316 Å2
2--0.8506 Å21.6424 Å2
3---0.7468 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: LAST / Resolution: 1.55→22.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 18 543 4995
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018970HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0816320HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2556SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1226HARMONIC5
X-RAY DIFFRACTIONt_it8970HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.27
X-RAY DIFFRACTIONt_other_torsion2.92
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_contact10107SEMIHARMONIC4
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2427 268 5.09 %
Rwork0.208 4999 -
all0.2097 5267 -
obs--95.86 %
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)
10.8752-0.3693-0.54371.36350.01411.3798-0.2119-0.0423-0.08870.0390.0817-0.08070.23070.09050.1302-0.09390.00870.0304-0.1045-0.0029-0.09424.7036-3.9538.3009
20.18760.2447-0.13591.72540.24491.0276-0.0142-0.02020.0018-0.04550.0788-0.1865-0.11030.0867-0.0646-0.09830.0151-0.0024-0.0502-0.017-0.04574.4379-19.67378.5814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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