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- PDB-4utp: Crystal structure of pneumococcal surface antigen PsaA in the Cd-... -

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Basic information

Entry
Database: PDB / ID: 4utp
TitleCrystal structure of pneumococcal surface antigen PsaA in the Cd- bound, closed 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: 2 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 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 28, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _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)73,27827
Polymers70,4682
Non-polymers2,81025
Water2,234124
1
A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,69514
Polymers35,2341
Non-polymers1,46113
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)36,58313
Polymers35,2341
Non-polymers1,34912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.239, 47.911, 101.524
Angle α, β, γ (deg.)90.00, 106.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35233.922 Da / Num. of mol.: 2
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.: 25 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST FIVE RESIDUES GNLYF ARE THE REMAINDER OF THE HIS- TAG CLEAVAGE SITE.

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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: 2.37 Å3/Da / Density % sol: 48.2 % / Description: NONE
Crystal growpH: 8
Details: 26-36 % PEG 400, 0.1 M NACL, 0.1 M TRIZMA-HCL PH 8.0 AND 0.1 M CDCL2

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→43 Å / Num. obs: 36157 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.24
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.13 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSZ

1psz


Resolution: 2→42.97 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.059 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26028 1814 5 %RANDOM
Rwork0.22052 ---
obs0.22249 34346 93.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.319 Å2
Baniso -1Baniso -2Baniso -3
1-20.12 Å20 Å2-14.71 Å2
2---16.33 Å20 Å2
3----3.79 Å2
Refinement stepCycle: LAST / Resolution: 2→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 25 124 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024608
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.9716222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49426.759216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24715864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.812154
X-RAY DIFFRACTIONr_chiral_restr0.0720.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213446
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2673.8162262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1045.7192824
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5563.9922346
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 121 -
Rwork0.308 2510 -
obs--93.07 %

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