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- PDB-5j1d: X-ray crystal structure of Phosphate binding protein (PBP) from S... -

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Basic information

Entry
Database: PDB / ID: 5j1d
TitleX-ray crystal structure of Phosphate binding protein (PBP) from Stenotrophomonas maltophilia
ComponentsPhosphate binding protein
KeywordsPROTEIN BINDING / Venus flytrap / ATP binding cassette / Serendipitous / Phosphate binding protein
Function / homologyPBP superfamily domain / PBP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / Alkaline phosphatase
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHatti, K. / Gulati, A. / Narayanswamy, S. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchBIC/11(25)/2014 India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Determination of crystal structures of proteins of unknown identity using a marathon molecular replacement procedure: structure of Stenotrophomonas maltophilia phosphate-binding protein.
Authors: Hatti, K. / Gulati, A. / Srinivasan, N. / Murthy, M.R.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)38,5204
Polymers38,2401
Non-polymers2793
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.780, 78.070, 56.380
Angle α, β, γ (deg.)90.000, 102.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphate binding protein


Mass: 38240.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Stenotrophomonas maltophilia (bacteria) / References: UniProt: A0A4T1DUK4*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-tris, pH 6.5, 20% PEG MME-5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→55.071 Å / Num. obs: 25257 / % possible obs: 100 % / Redundancy: 4.9 % / Rsym value: 0.08 / Net I/av σ(I): 8.805 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-24.70.2183.51100
2-2.124.80.1644.61100
2.12-2.274.80.1325.71100
2.27-2.454.90.116.91100
2.45-2.694.90.0937.91100
2.69-34.90.073101100
3-3.4750.05313.11100
3.47-4.2550.04514.51100
4.25-6.0150.035181100
6.01-39.0354.90.03117.5199.7

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q9T, 2V3Q, 4F1V, 4M1V

2q9t

2v3q

4f1v

4m1v


Resolution: 1.9→55.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.098 / SU ML: 0.063 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1512 1286 5.1 %RANDOM
Rwork0.1221 ---
obs0.1236 23949 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.83 Å2 / Biso mean: 8.864 Å2 / Biso min: 2.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.9→55.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 17 427 3142
Biso mean--14.62 20.41 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022800
X-RAY DIFFRACTIONr_bond_other_d0.0010.022587
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9463834
X-RAY DIFFRACTIONr_angle_other_deg0.79335944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6915378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50524.327104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27415381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3721511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213294
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02643
X-RAY DIFFRACTIONr_mcbond_it0.3780.7851506
X-RAY DIFFRACTIONr_mcbond_other0.3770.7851505
X-RAY DIFFRACTIONr_mcangle_it0.6351.1751886
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 97 -
Rwork0.145 1749 -
all-1846 -
obs--100 %

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