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- PDB-4x9t: Crystal structure of a TctC solute binding protein from Polaromon... -

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Basic information

Entry
Database: PDB / ID: 4x9t
TitleCrystal structure of a TctC solute binding protein from Polaromonas (Bpro_3516, Target EFI-510338), no ligand
ComponentsUncharacterized protein UPF0065
KeywordsUNKNOWN FUNCTION / Solute binding protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


Bordetella uptake gene, domain 1 / Bordetella uptake gene / Bordetella uptake gene, domain 1 / Tripartite tricarboxylate transporter family receptor / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein UPF0065
Similarity search - Component
Biological speciesPolaromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of a TctC solute binding protein from Polaromonas (Bpro_3516, Target EFI-510338), no ligand
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 11, 2015Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein UPF0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4214
Polymers34,3151
Non-polymers1063
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.976, 79.244, 111.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a MONOMER

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Components

#1: Protein Uncharacterized protein UPF0065


Mass: 34314.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. (strain JS666 / ATCC BAA-500) (bacteria)
Strain: JS666 / ATCC BAA-500 / Gene: Bpro_3516 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q126W8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (77.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT), Reservoir (MCSG 1, H10, 0.1 M HEPES pH 7.5, 25 %(w/v) PEG 3350), Cryoprotection (Reservoir,dehydrated)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 12, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.24→100 Å / Num. obs: 71858 / % possible obs: 88.1 % / Redundancy: 7 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.081 / Χ2: 0.895 / Net I/av σ(I): 18.29 / Net I/σ(I): 9.2 / Num. measured all: 500010
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.24-1.266.70.87135300.84589.1
1.26-1.286.70.80135250.8686.8
1.28-1.316.50.69335100.87288.4
1.31-1.346.50.60834820.87585.6
1.34-1.366.40.54334860.87387.5
1.36-1.46.30.45534150.89584
1.4-1.436.20.36634290.88885.7
1.43-1.476.10.32433860.88883.7
1.47-1.5160.25934200.87684.6
1.51-1.5660.21433700.88183.8
1.56-1.6260.17433580.85282.5
1.62-1.686.10.14533980.81483.4
1.68-1.766.30.12134210.79384.3
1.76-1.856.60.10334650.79585.6
1.85-1.976.90.09836250.98388.8
1.97-2.127.30.10137641.33891.7
2.12-2.337.90.09738251.44393.2
2.33-2.678.50.06839740.87895.4
2.67-3.3790.05141280.64799
3.37-1009.70.04643470.66698.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.24→22.81 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 3154 4.98 %
Rwork0.1634 60168 -
obs0.1647 63322 77.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.82 Å2 / Biso mean: 21.0398 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: final / Resolution: 1.24→22.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 3 377 2542
Biso mean--26.91 30.19 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052225
X-RAY DIFFRACTIONf_angle_d1.0273031
X-RAY DIFFRACTIONf_chiral_restr0.039347
X-RAY DIFFRACTIONf_plane_restr0.006393
X-RAY DIFFRACTIONf_dihedral_angle_d12.851800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.24-1.25840.2795370.225478281924
1.2584-1.27810.2727470.21991059110632
1.2781-1.2990.2737850.20991397148243
1.299-1.32140.21721020.20751832193456
1.3214-1.34540.21331180.20262253237168
1.3454-1.37130.2311360.19592488262476
1.3713-1.39930.21141360.19572606274278
1.3993-1.42970.2011590.18952683284282
1.4297-1.4630.20641580.20442700285881
1.463-1.49950.20471480.17642751289983
1.4995-1.54010.20751460.17242766291283
1.5401-1.58540.15551220.16862838296084
1.5854-1.63650.18581530.16592762291583
1.6365-1.6950.18691540.16662795294983
1.695-1.76290.18271500.16982817296784
1.7629-1.84310.19111690.1732852302186
1.8431-1.94020.19031450.1722951309688
1.9402-2.06170.21441750.16493085326092
2.0617-2.22070.16781390.1643145328492
2.2207-2.4440.18771550.16473243339894
2.444-2.79710.20091660.17863314348097
2.7971-3.52190.18761650.16023475364099
3.5219-22.81350.17771890.14053574376399
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)
11.53830.1428-0.33691.4524-0.03511.51450.01380.0455-0.028-0.0054-0.03930.10240.073-0.16080.02140.13290.0049-0.01010.1467-0.01560.138111.972632.146519.8249
21.3086-0.1156-1.27520.4067-0.14983.5319-0.0492-0.0630.00150.0584-0.0302-0.02090.0212-0.04880.06180.1279-0.0038-0.01160.1166-0.00040.145711.127941.517353.0721
32.4688-1.22380.12842.2457-0.11761.72-0.03760.0405-0.0070.00430.03010.0230.0816-0.1184-0.01290.119-0.0293-0.00140.1487-0.00520.13412.326937.059248.4184
42.7573-0.1548-0.70251.11690.04191.51630.00760.05640.0782-0.001-0.0205-0.042-0.06430.02670.00830.1374-0.0048-0.01330.14140.00230.125413.290745.306646.621
50.3199-0.0527-0.38430.23250.78383.76330.0088-0.0143-0.04890.0797-0.0054-0.0690.25250.0145-0.00940.1621-0.0013-0.0040.11740.00360.160916.968230.595735.8462
61.673-0.7155-0.62081.09660.2481.7190.0707-0.04410.16640.0498-0.0038-0.1121-0.20010.0361-0.08150.149-0.00930.00290.12710.00160.153522.262840.054123.9259
79.56772.9667-6.71453.6023-2.55388.5580.0213-0.1537-0.00050.2399-0.11960.27430.2115-0.1390.11510.222-0.03410.01860.1686-0.02150.159213.010424.697137.4644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 119 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 147 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 193 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 235 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 257 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 292 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 293 through 314 )A0

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