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- PDB-3s4u: Crystal structure of open, unliganded E. coli PhnD H157A -

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Basic information

Entry
Database: PDB / ID: 3s4u
TitleCrystal structure of open, unliganded E. coli PhnD H157A
ComponentsPhnD, subunit of alkylphosphonate ABC transporter
KeywordsTRANSPORT PROTEIN / Phosphonate binding / Globular protein
Function / homology
Function and homology information


organic phosphonate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Phosphonate ABC transporter, substrate-binding protein / Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PhnD, subunit of alkylphosphonate ABC transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAlicea, I. / Schreiter, E.R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of the Escherichia coli Phosphonate Binding Protein PhnD and Rationally Optimized Phosphonate Biosensors.
Authors: Alicea, I. / Marvin, J.S. / Miklos, A.E. / Ellington, A.D. / Looger, L.L. / Schreiter, E.R.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PhnD, subunit of alkylphosphonate ABC transporter


Theoretical massNumber of molelcules
Total (without water)35,7411
Polymers35,7411
Non-polymers00
Water0
1
A: PhnD, subunit of alkylphosphonate ABC transporter

A: PhnD, subunit of alkylphosphonate ABC transporter


Theoretical massNumber of molelcules
Total (without water)71,4832
Polymers71,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation7_565y,x+1,-z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.735, 103.735, 58.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein PhnD, subunit of alkylphosphonate ABC transporter


Mass: 35741.379 Da / Num. of mol.: 1 / Fragment: UNP residues 27-338 / Mutation: H157A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: phnD, UTI89_C4699 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q1R3F7

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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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 20, 2010
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 5149 / Num. obs: 5123 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
SPECdata collection
PHASERfor MRphasing
REFMAC5.6.0111refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.824 / SU B: 70.628 / SU ML: 0.532 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.676 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28867 237 4.6 %RANDOM
Rwork0.19376 ---
all0.19833 5149 --
obs0.19833 4867 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å2-0 Å2-0 Å2
2--1.61 Å20 Å2
3----3.21 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 0 0 2360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222406
X-RAY DIFFRACTIONr_bond_other_d0.0020.021631
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9583259
X-RAY DIFFRACTIONr_angle_other_deg1.00934008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5775301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.23825.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.16715426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.052159
X-RAY DIFFRACTIONr_chiral_restr0.090.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212676
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02457
LS refinement shellResolution: 3.3→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 17 -
Rwork0.201 290 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -5.836 Å / Origin y: -27.162 Å / Origin z: -5.571 Å
111213212223313233
T0.0193 Å20.0178 Å20.0034 Å2-0.0423 Å20.0126 Å2--0.0879 Å2
L1.9669 °20.113 °2-0.7312 °2-1.2098 °2-0.5079 °2--2.37 °2
S0.0764 Å °-0.1064 Å °-0.0947 Å °-0.1012 Å °-0.0889 Å °-0.0279 Å °0.1236 Å °0.31 Å °0.0124 Å °

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