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- PDB-1psz: PNEUMOCOCCAL SURFACE ANTIGEN PSAA -

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Basic information

Entry
Database: PDB / ID: 1psz
TitlePNEUMOCOCCAL SURFACE ANTIGEN PSAA
ComponentsPROTEIN (SURFACE ANTIGEN PSAA)
KeywordsIMMUNE SYSTEM / PSAA / ABC-TYPE BINDING PROTEIN / METAL-BINDING PROTEIN / PNEUMOCOCCAL SURFACE ANTIGEN
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 / MIR / Resolution: 2 Å
AuthorsLawrence, M.C. / Pilling, P.A. / Epa, V.C. / Berry, A.M. / Ogunniyi, A.D. / Paton, J.C.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Expression, Purification and Preliminary X-Ray Crystallographic Analysis of PsaA, a Putative Metal-Transporter Protein of Streptococcus Pnuemoniae
Authors: Pilling, P.A. / Lawrence, M.C. / Berry, A.M. / Ogunniyi, A.D. / Lock, R.A. / Paton, J.C.
History
DepositionOct 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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

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Assembly

Deposited unit
A: PROTEIN (SURFACE ANTIGEN PSAA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2092
Polymers34,1431
Non-polymers651
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.024, 66.517, 69.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (SURFACE ANTIGEN PSAA)


Mass: 34143.254 Da / Num. of mol.: 1
Mutation: INCLUDES N-TERMINAL PURIFICATION TAG WRGSHHHHHHGSA
Source method: isolated from a genetically manipulated source
Details: THE EXPRESSED CONSTRUCT LACKS THE PRO-LIPOPROTEIN RECOGNITION SEQUENCE LXXC
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 (SEROTYPE 2) / Cellular location: EXTRACELLULAR / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): SG12009 [PREP4] / References: UniProt: P0A4G2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DATABASE ENTRY HAS RESIDUES 1 TO 309 THE CRYSTALLIZED PROTEIN HAS RESIDUES 20 TO 309 PRECEDED ...THE DATABASE ENTRY HAS RESIDUES 1 TO 309 THE CRYSTALLIZED PROTEIN HAS RESIDUES 20 TO 309 PRECEDED BY A 13 RESIDUE PURIFICATION TAG COORDINATES ARE PROVIDED FOR RESIDUES 24 TO 309

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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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN BY MICRO OR MACROSEEDING IN HANGING DROPS. PROTEIN CONCENTRATION 18 MG/ML. PRECIPITANT 3.0 M K2HPO4/NAH2PO4 (PH 7.5) 0.1 M MES ( PH 6.5) 0.1 M GUHCL AT 18 DEGREES.
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: Pilling, P.A., (1998) Acta Crystallogr., Sect.D, 54, 1464.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13.0 Msodium potassium phosphate1droppH7.5
20.1 MMES1droppH6.5
30.1 M1dropGuHCl
43.0 Msodium potassium phosphate1reservoirpH7.5
50.1 MMES1reservoirpH6.5
60.1 M1reservoirGuHCl

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 19354 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.4 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→8 Å / SU B: 3.9 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.18
Details: NO STEREOCHEMICAL CONSTRAINTS WERE APPLIED TO THE ZINC ION DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.236 979 5 %RANDOM
Rwork0.178 ---
obs-19029 99.98 %-
Displacement parametersBiso mean: 17.3 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 1 225 2502
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.262
X-RAY DIFFRACTIONp_mcangle_it1.9443
X-RAY DIFFRACTIONp_scbond_it1.6012
X-RAY DIFFRACTIONp_scangle_it2.5053
X-RAY DIFFRACTIONp_plane_restr0.0215
X-RAY DIFFRACTIONp_chiral_restr0.1010.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2530.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1260.3
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor18.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.3 Å2
Refine LS restraints
*PLUS
Type: p_mcbond_it / Dev ideal target: 2

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