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- PDB-4n6d: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4n6d
TitleCrystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio salexigens DSM2638 (Desal_3247), Target EFI-510112, phased with I3C, open complex, C-terminus of symmetry mate bound in ligand binding site
ComponentsTRAP dicarboxylate transporter-DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-I3C / TRAP dicarboxylate transporter-DctP subunit
Similarity search - Component
Biological speciesDesulfovibrio salexigens (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.701 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. ...Vetting, M.W. / Al Obaidi, N.F. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 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: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4955
Polymers38,2801
Non-polymers1,2154
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.703, 68.249, 108.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRAP dicarboxylate transporter-DctP subunit / TRAP periplasmic solute binding protein


Mass: 38280.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio salexigens (bacteria) / Strain: ATCC 14822 / DSM 2638 / NCIB 8403 / VKM B-1763 / Gene: Desal_3247 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6C297
#2: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Tryptophan, reservoir: 0.1 M tri-sodium citrate, pH 5.5, 20% w/v PEG3000, soak for 5 minutes in 250 mM IC3, 20% PEG3350, 100 mM ...Details: 40 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-Tryptophan, reservoir: 0.1 M tri-sodium citrate, pH 5.5, 20% w/v PEG3000, soak for 5 minutes in 250 mM IC3, 20% PEG3350, 100 mM HEPES, pH 7.0, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 9, 2013 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 36699 / Num. obs: 36699 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Χ2: 2.083 / Net I/σ(I): 22.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.738.10.23715541.106184.9
1.73-1.769.40.20617171.199193.4
1.76-1.7911.90.18217681.327196.7
1.79-1.8312.60.16418211.517199.9
1.83-1.8712.20.15518011.635197.5
1.87-1.9112.60.13118321.514199.6
1.91-1.9612.60.11418051.678198.2
1.96-2.0212.50.09818421.752199.6
2.02-2.0712.60.08818241.877199
2.07-2.1412.40.07618462.002199.2
2.14-2.2212.40.07118342.084199.9
2.22-2.3112.40.06518412.106199.6
2.31-2.4112.40.06318512.193199.7
2.41-2.5412.40.05918732.342199.9
2.54-2.712.60.05618632.3841100
2.7-2.9112.90.0518862.4111100
2.91-3.213.50.04318902.3381100
3.2-3.6614.10.03619102.1321100
3.66-4.6114.10.03419122.53199.7
4.61-10013.30.0420294.173198.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.701→21.982 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.9061 / SU ML: 0.14 / σ(F): 0 / σ(I): 0 / Phase error: 15.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 1834 5.01 %RANDOM
Rwork0.1453 ---
all0.1472 36641 --
obs0.1472 36641 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.68 Å2 / Biso mean: 18.3755 Å2 / Biso min: 5.87 Å2
Refinement stepCycle: LAST / Resolution: 1.701→21.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 37 421 2955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092613
X-RAY DIFFRACTIONf_angle_d1.2133543
X-RAY DIFFRACTIONf_chiral_restr0.068389
X-RAY DIFFRACTIONf_plane_restr0.006452
X-RAY DIFFRACTIONf_dihedral_angle_d12.271984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74650.20851380.16072264240285
1.7465-1.79790.21151370.15762583272096
1.7979-1.85590.21561370.14992670280799
1.8559-1.92220.19551250.14972638276399
1.9222-1.99910.22571390.14882707284699
1.9991-2.090.18721420.13842666280899
2.09-2.20010.17261470.13192686283399
2.2001-2.33780.16291350.131627092844100
2.3378-2.5180.18591340.131527232857100
2.518-2.7710.17931540.147527142868100
2.771-3.17090.15721220.150827742896100
3.1709-3.99110.17351430.142227962939100
3.9911-21.98350.18981810.156928773058100
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)
10.9631-0.38670.13230.8302-0.31230.3457-0.0245-0.02250.0565-0.00480.02670.0099-0.0125-0.0329-0.00460.0703-0.00680.00080.0665-0.01310.07159.754736.2962-0.3152
20.30080.25170.3011.22610.14940.9528-0.0043-0.1216-0.01480.1745-0.05250.33840.1373-0.25340.03940.1452-0.01560.04730.1707-0.01680.14799.272219.354521.9447
30.2889-0.20630.28850.4239-0.28120.7634-0.0296-0.06680.05680.01030.0133-0.00810.0278-0.06620.020.0695-0.00450.00060.0812-0.01430.081911.153832.19989.1118
40.3741-0.0391-0.05140.6577-1.09262.8819-0.0284-0.05080.09540.1838-0.0337-0.0375-0.27210.11160.02660.1165-0.0056-0.00650.0838-0.01590.11317.259340.48211.0295
50.0311-0.0687-0.04440.12210.07910.5535-0.0621-0.0077-00.10070.03580.0380.17040.27570.01080.10490.03110.0070.13910.00450.111120.228215.46812.0293
61.32720.3638-0.25840.9504-0.05830.12840.0082-0.1270.02410.11460.0525-0.2471-0.02510.1991-0.05280.08820.011-0.00770.1391-0.00210.162132.519125.09784.2769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 146 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 215 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 216 through 248 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 285 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 286 through 318 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 319 through 346 )A0

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