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- PDB-1a55: PHOSPHATE-BINDING PROTEIN MUTANT A197C -

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Basic information

Entry
Database: PDB / ID: 1a55
TitlePHOSPHATE-BINDING PROTEIN MUTANT A197C
ComponentsPHOSPHATE-BINDING PROTEIN
KeywordsPHOSPHOTRANSFERASE / TRANSPORT
Function / homology
Function and homology information


regulation of phosphatase activity / phosphate ion transport / phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / Phosphate-binding protein PstS / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.4 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: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5872
Polymers34,4901
Non-polymers971
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.040, 64.161, 124.353
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


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) / Strain: PAN92 / Cell line: AN2538 / Cellular location: PERIPLASM / Gene: PHO-S / Cell line (production host): AN2538 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): PIBI24 / References: UniProt: P06128, UniProt: P0AG82*PLUS
#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
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: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25.4 Å / Num. obs: 70788 / % possible obs: 86.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.047
Reflection shellHighest resolution: 2.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.19 / % possible all: 69.2
Reflection
*PLUS
Num. obs: 10913 / Num. measured all: 70788
Reflection shell
*PLUS
% possible obs: 69.2 % / Mean I/σ(I) obs: 4.2

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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: 2.4→12 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -5 %RANDOM
Rwork0.173 ---
obs-10913 86.6 %-
Refinement stepCycle: LAST / Resolution: 2.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 5 268 2718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d3.204
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: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.2 Å2

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