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- PDB-4qhq: The structure of a nutrient binding protein from Burkholderia cen... -

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Basic information

Entry
Database: PDB / ID: 4qhq
TitleThe structure of a nutrient binding protein from Burkholderia cenocepacia bound to methionine
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / nutrient binding protein / ABC transporter / methionine
Function / homology
Function and homology information


Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE / DI(HYDROXYETHYL)ETHER / Lipoprotein
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: The structure of a nutrient binding protein from Burkholderia cenocepacia bound to methionine
Authors: Clifton, M.C. / Arakaki, T.
History
DepositionMay 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3923
Polymers26,1371
Non-polymers2552
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.630, 67.170, 55.480
Angle α, β, γ (deg.)90.000, 101.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipoprotein


Mass: 26136.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAL0763 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EA88
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20mg/ml BuceA.18560.a.B1.PS01924, 100mM succinic acid, 15% PEG3350, 20% Ethylene glycol as a cryoprotectant, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.4→28.57 Å / Num. obs: 43114 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.61 Å2 / Rmerge(I) obs: 0.042 / Χ2: 1.023 / Net I/σ(I): 19.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.440.2755.1314885306492.3
1.44-1.480.2266.4615294304096.5
1.48-1.520.2037.4815036298494.5
1.52-1.570.169.4814621290995.8
1.57-1.620.13910.7614280285496.4
1.62-1.670.11213.0313648272295.2
1.67-1.740.0951513130265697.3
1.74-1.810.07717.9212667256196.8
1.81-1.890.06620.412015245296.3
1.89-1.980.05823.3111443237196.6
1.98-2.090.0526.410819224798.6
2.09-2.210.04529.3110276212797.6
2.21-2.370.04330.859691202297.7
2.37-2.560.0432.229112189298.3
2.56-2.80.03734.28485174898.3
2.8-3.130.03335.557662157598.8
3.13-3.610.0337.276848139598.4
3.61-4.430.02337.665762119098.9
4.43-6.260.02137.05430291096.7
6.260.02134.81169539575.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.4 Å42.25 Å
Translation1.4 Å42.25 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TQW

3tqw


Resolution: 1.4→28.57 Å / SU ML: 0.12 / σ(F): 1.39 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 2175 5.05 %
Rwork0.167 --
obs0.1683 43073 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.26 Å2 / Biso mean: 21.3156 Å2 / Biso min: 6.58 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 16 257 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051838
X-RAY DIFFRACTIONf_angle_d1.0932511
X-RAY DIFFRACTIONf_chiral_restr0.076298
X-RAY DIFFRACTIONf_plane_restr0.006331
X-RAY DIFFRACTIONf_dihedral_angle_d12.333664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.43040.24411300.21372426255692
1.4304-1.46370.21411300.19922530266096
1.4637-1.50030.22741270.19662494262194
1.5003-1.54090.23491340.18532559269397
1.5409-1.58620.2291390.17852506264594
1.5862-1.63740.22191410.17812559270097
1.6374-1.69590.18991490.1712498264796
1.6959-1.76380.20881280.16942557268596
1.7638-1.84410.18651360.17092589272597
1.8441-1.94130.18921410.17082559270097
1.9413-2.06290.19291310.1762602273397
2.0629-2.22210.22991460.16662580272698
2.2221-2.44560.19881440.1732589273398
2.4456-2.79920.21071440.17582639278399
2.7992-3.52570.17991360.15672647278399
3.5257-28.57580.15311190.14382564268394
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)
13.1521-0.7221.20492.8689-0.27914.24870.0061-0.2482-0.26870.27250.0603-0.00880.32860.0551-0.07730.1481-0.00590.01190.11170.05480.1362-9.3360.2665.017
21.8751-0.64330.64882.1527-0.3253.2461-0.0763-0.4042-0.16950.23610.13770.1906-0.0094-0.3607-0.0530.10660.01180.02410.1990.02880.1146-15.8799.5267.284
32.1044-0.56120.6765.10150.23843.0228-0.1477-0.16410.18960.10940.11050.0381-0.4266-0.0750.04120.10780.0118-0.01540.0822-0.01630.0843-12.79618.968-0.92
41.6967-0.10531.06931.08810.40572.9379-0.05890.19210.0325-0.2117-0.0370.0226-0.3566-0.07160.08480.11960.00940.00570.1087-0.00980.0876-16.27614.126-16.491
52.17730.0364-1.08442.3939-1.11142.57240.02150.11180.1982-0.3741-0.1002-0.091-0.8524-0.02420.08850.52190.0238-0.03220.1761-0.01570.1774-18.77623.867-20.9
62.1061-0.55690.9481.3853-0.0342.54450.06540.1745-0.2309-0.1097-0.02220.09470.0412-0.0967-0.03020.0722-0.0010.00650.1057-0.02920.1144-17.6467.449-15.867
72.3308-0.99090.50142.45840.81624.6974-0.0892-0.35720.06730.33850.1629-0.2725-0.00720.187-0.08460.1021-0.0122-0.03070.15780.00080.1105-2.87410.4238.015
82.9078-0.04851.61452.548-0.81494.10790.12160.0436-0.3207-0.0468-0.03-0.160.38980.2991-0.08870.13730.02860.00710.1357-0.02880.1964-4.029-0.856-7.183
97.551-1.8457-5.85017.36452.79814.8390.0909-0.01930.1075-0.17040.0313-0.1995-0.12590.1826-0.13130.0787-0.00410.00390.1191-0.00950.1135-13.14411.829-7.298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 31:56 )A31 - 56
2X-RAY DIFFRACTION2( CHAIN A AND RESID 57:81 )A57 - 81
3X-RAY DIFFRACTION3( CHAIN A AND RESID 82:98 )A82 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:150 )A99 - 150
5X-RAY DIFFRACTION5( CHAIN A AND RESID 151:185 )A151 - 185
6X-RAY DIFFRACTION6( CHAIN A AND RESID 186:228 )A186 - 228
7X-RAY DIFFRACTION7( CHAIN A AND RESID 229:252 )A229 - 252
8X-RAY DIFFRACTION8( CHAIN A AND RESID 253:271 )A253 - 271
9X-RAY DIFFRACTION9( CHAIN A AND RESID 301:301 )A301

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