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- PDB-1a54: PHOSPHATE-BINDING PROTEIN MUTANT A197C LABELLED WITH A COUMARIN F... -

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Basic information

Entry
Database: PDB / ID: 1a54
TitlePHOSPHATE-BINDING PROTEIN MUTANT A197C LABELLED WITH A COUMARIN FLUOROPHORE AND BOUND TO DIHYDROGENPHOSPHATE ION
ComponentsPhosphate-binding protein PstS
KeywordsPHOSPHOTRANSFERASE / TRANSPORT / COUMARIN / FLUOROPHORE
Function / homology
Function and homology information


phosphate ion transport / phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / response to radiation / outer membrane-bounded periplasmic space / DNA damage response / membrane
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / : / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / Chem-MDC / Phosphate-binding protein PstS / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.6 Å
AuthorsHirshberg, M. / Henrick, K. / Lloyd-Haire, L. / Vasisht, N. / Brune, M. / Corrie, J.E.T. / Webb, M.R.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structure of phosphate binding protein labeled with a coumarin fluorophore, a probe for inorganic phosphate.
Authors: Hirshberg, M. / Henrick, K. / Haire, L.L. / Vasisht, N. / Brune, M. / Corrie, J.E. / Webb, M.R.
#1: Journal: Biochemistry / Year: 1998
Title: Mechanism of Inorganic Phosphate Interaction with Phosphate Binding Protein from Escherichia Coli
Authors: Brune, M. / Hunter, J.L. / Howell, S.A. / Martin, S.R. / Hazlett, T.L. / Corrie, J.E. / Webb, M.R.
History
DepositionFeb 19, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Aug 10, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_sheet.id / _struct_sheet.number_strands
Revision 2.1Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Dec 25, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9703
Polymers34,4901
Non-polymers4802
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.498, 62.651, 122.608
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 Phosphate-binding protein PstS


Mass: 34489.664 Da / Num. of mol.: 1 / Mutation: A197C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: AN2538 / Cellular location: PERIPLASM / Gene: pstS, BvCmsKKP036_01783, EYX47_15990 / Cell line (production host): AN2538 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): PIBI24 / References: UniProt: A0A4S1QQS5, UniProt: P0AG82*PLUS
#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#3: Chemical ChemComp-MDC / N-[2-(1-MALEIMIDYL)ETHYL]-7-DIETHYLAMINOCOUMARIN-3-CARBOXAMIDE


Mass: 383.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
210 mMTris-HCl1drop
320-24 %(w/v)PEG60001reservoir
420 mMpotassium acetate1reservoir
52 mMpotassium phosphate1reservoir
650 mM1reservoirKCl

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.6→12 Å / Num. obs: 345731 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08
Reflection shellHighest resolution: 1.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.21 / % possible all: 93.4
Reflection
*PLUS
Num. obs: 40945 / Num. measured all: 345731
Reflection shell
*PLUS
% possible obs: 93.4 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
CCP4model building
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 2ABH

2abh


Resolution: 1.6→12 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.208 -5 %RANDOM
Rwork0.177 ---
obs-40945 95.5 %-
Refinement stepCycle: LAST / Resolution: 1.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 41 334 2817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d1.859
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.9 Å2

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