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- PDB-3p7i: Crystal structure of Escherichia coli PhnD in complex with 2-amin... -

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Basic information

Entry
Database: PDB / ID: 3p7i
TitleCrystal structure of Escherichia coli PhnD in complex with 2-aminoethyl phosphonate
ComponentsPhnD, subunit of alkylphosphonate ABC transporter
KeywordsTRANSPORT PROTEIN / Phosphonate binding 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
(2-aminoethyl)phosphonic acid / PhnD, subunit of alkylphosphonate ABC transporter
Similarity search - Component
Biological speciesEscherichia coli UTI89 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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: PhnD, subunit of alkylphosphonate ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2105
Polymers35,8081
Non-polymers4014
Water2,576143
1
A: PhnD, subunit of alkylphosphonate ABC transporter
hetero molecules

A: PhnD, subunit of alkylphosphonate ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,42010
Polymers71,6172
Non-polymers8038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3410 Å2
ΔGint-13 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.094, 82.440, 54.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PhnD, subunit of alkylphosphonate ABC transporter


Mass: 35808.449 Da / Num. of mol.: 1 / Fragment: UNP residues 27-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Strain: UTI89 / UPEC / Gene: phnD, UTI89_C4699 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1R3F7
#2: Chemical ChemComp-P7I / (2-aminoethyl)phosphonic acid


Mass: 125.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H8NO3P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M ammonium sulfate, sodium acetate trihydrate, pH 4.6, 25% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2009
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.71→45.6 Å / Num. all: 35864 / Num. obs: 35721 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
SPECdata collection
PHASERphasing
REFMAC5.5.0072refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→45.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25144 1880 5 %RANDOM
Rwork0.22568 ---
all0.22697 35864 --
obs0.22697 35721 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.239 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.71→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 25 143 2521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222603
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.973542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.22825.798119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72815478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9941511
X-RAY DIFFRACTIONr_chiral_restr0.1510.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211959
X-RAY DIFFRACTIONr_mcbond_it1.3191.51598
X-RAY DIFFRACTIONr_mcangle_it2.07722594
X-RAY DIFFRACTIONr_scbond_it3.21531005
X-RAY DIFFRACTIONr_scangle_it5.0514.5933
LS refinement shellResolution: 1.71→1.757 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 119 -
Rwork0.445 2547 -
obs--97.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.03590.652-1.11251.5976-0.67441.0811-0.0973-0.2541-0.1949-0.0158-0.0908-0.27960.06990.19080.18810.03140.0081-0.03190.06270.05380.127311.935-26.94915.441
22.01290.59020.41540.76050.30130.61950.0779-0.0639-0.11780.091-0.0350.02540.0474-0.0558-0.04290.0373-0.0047-0.02260.02750.02320.0915-9.11-25.74812.385
31.65320.3844-0.70391.96360.03230.3382-0.02380.00190.0273-0.03360.0285-0.0515-0.01810.0275-0.00460.0578-0.0151-0.01840.05690.00850.10147.769-14.77210.181
46.3889-5.1237-5.94714.96992.491311.98580.1420.17150.26230.05390.1748-0.1387-0.2473-0.9538-0.31670.20740.03720.08120.13910.11450.3677-26.981-8.25523.947
52.98190.4076-2.27834.9123-2.01044.3502-0.0054-0.0438-0.40340.2254-0.07880.4585-0.0191-0.02890.08430.0547-0.02130.01820.0120.01210.2384-12.8790.27914.997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 41
2X-RAY DIFFRACTION2A42 - 211
3X-RAY DIFFRACTION3A212 - 263
4X-RAY DIFFRACTION4A264 - 281
5X-RAY DIFFRACTION5A282 - 304

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