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- PDB-4pqj: Crystal structure of a phosphate binding protein -

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Basic information

Entry
Database: PDB / ID: 4pqj
TitleCrystal structure of a phosphate binding protein
ComponentsPhosphate binding protein
KeywordsTRANSPORT PROTEIN / psts / phosphate binding / biofilm / substrate binding protein / phosphate transport
Function / homology
Function and homology information


phosphate ion transport / single-species biofilm formation / phosphate ion binding / periplasmic space / cell adhesion / extracellular region
Similarity search - Function
Phosphate binding protein / : / 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
PHOSPHATE ION / Phosphate-binding protein PstS / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsOpatowsky, Y. / Neznansky, A.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a phosphate binding protein
Authors: Opatowsky, Y. / Neznansky, A.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phosphate binding protein
C: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5434
Polymers64,3532
Non-polymers1902
Water7,152397
1
A: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2722
Polymers32,1771
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2722
Polymers32,1771
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.500, 151.350, 108.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

21A-613-

HOH

31C-689-

HOH

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Components

#1: Protein Phosphate binding protein / PstS


Mass: 32176.600 Da / Num. of mol.: 2 / Fragment: UNP residues 25-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pstS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z9M3, UniProt: P0DMR4*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG 3350, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.86→62.16 Å / Num. all: 47406 / Num. obs: 47406 / % possible obs: 100 % / Observed criterion σ(F): 94280 / Observed criterion σ(I): 94280 / Redundancy: 2 % / Biso Wilson estimate: 24.67 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.08
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.86-1.921100
1.92-1.961100
1.96-2.01199.9
2.01-2.06199
2.06-2.11197.7
2.11-2.171100

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→62.159 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 29.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1998 4.22 %RANDOM
Rwork0.216 ---
obs0.218 47378 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→62.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 10 397 4504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094173
X-RAY DIFFRACTIONf_angle_d1.2395653
X-RAY DIFFRACTIONf_dihedral_angle_d13.7561539
X-RAY DIFFRACTIONf_chiral_restr0.048637
X-RAY DIFFRACTIONf_plane_restr0.007723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90140.40131410.37463191X-RAY DIFFRACTION100
1.9014-1.95280.39521410.39283219X-RAY DIFFRACTION100
1.9528-2.01030.39571440.36073246X-RAY DIFFRACTION100
2.0103-2.07520.36761380.33963181X-RAY DIFFRACTION99
2.0752-2.14930.33141380.3033128X-RAY DIFFRACTION98
2.1493-2.23540.31731440.28313249X-RAY DIFFRACTION100
2.2354-2.33710.35391420.27013218X-RAY DIFFRACTION100
2.3371-2.46040.29551420.23583218X-RAY DIFFRACTION100
2.4604-2.61450.26731420.21853224X-RAY DIFFRACTION99
2.6145-2.81640.24931430.20693244X-RAY DIFFRACTION100
2.8164-3.09980.25881440.20253275X-RAY DIFFRACTION100
3.0998-3.54830.21711420.1823254X-RAY DIFFRACTION99
3.5483-4.47030.22661460.15243300X-RAY DIFFRACTION100
4.4703-62.19350.19971510.16253433X-RAY DIFFRACTION100

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