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- PDB-4xf5: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Entry
Database: PDB / ID: 4xf5
TitleCrystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0678), Target EFI-501078, with bound (S)-(+)-2-Amino-1-propanol.
ComponentsTwin-arginine translocation pathway signal
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


organic substance transport / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-aminopropan-1-ol / Twin-arginine translocation pathway signal
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsVetting, 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. ...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 TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0678), Target EFI-501078, with bound (S)-(+)-2-Amino-1-propanol.
Authors: 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, ...Authors: 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 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Experimental preparation
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Twin-arginine translocation pathway signal
B: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7738
Polymers79,4812
Non-polymers2926
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-75 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.605, 51.154, 111.943
Angle α, β, γ (deg.)90.000, 115.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-521-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein Twin-arginine translocation pathway signal


Mass: 39740.363 Da / Num. of mol.: 2 / Fragment: UNP residues 27-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (strain DSM 3043 / ATCC BAA-138 / NCIMB 13768) (bacteria)
Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_0678 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1QZR9
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-2A1 / (2S)-2-aminopropan-1-ol


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (60.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM S-Alaninol); Reservoir (MCSG1(C6), 0.2 M Magnesium Chloride, 0.1 M HEPES pH 7.5, 30 %(v/v) PPG P 400); Cryoprotection (Reservoir Solution)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→100.65 Å / Num. obs: 99699 / % possible obs: 90 % / Redundancy: 2.9 % / Biso Wilson estimate: 14.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.032 / Net I/σ(I): 12 / Num. measured all: 292987 / Scaling rejects: 40
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.45-1.4720.5571.5564928920.6410.46453.1
7.94-100.653.30.02432.123086950.9980.01594.7

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UAB

4uab


Resolution: 1.45→27.559 Å / FOM work R set: 0.8668 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 4973 4.99 %
Rwork0.1639 94695 -
obs0.1653 99668 90.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.84 Å2 / Biso mean: 23 Å2 / Biso min: 7.98 Å2
Refinement stepCycle: final / Resolution: 1.45→27.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 0 14 526 5666
Biso mean--15.78 30.08 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015307
X-RAY DIFFRACTIONf_angle_d1.2577223
X-RAY DIFFRACTIONf_chiral_restr0.074753
X-RAY DIFFRACTIONf_plane_restr0.008936
X-RAY DIFFRACTIONf_dihedral_angle_d14.0181888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46650.3345980.27391802190052
1.4665-1.48370.29721080.26831971207957
1.4837-1.50180.28981220.25732235235764
1.5018-1.52080.29331100.24572379248969
1.5208-1.54080.27281220.24092662278475
1.5408-1.5620.29321380.22362900303884
1.562-1.58430.22491740.21153019319386
1.5843-1.60790.23551560.20643104326089
1.6079-1.6330.23181700.20123177334791
1.633-1.65980.22561490.19223187333691
1.6598-1.68840.20281920.19043214340693
1.6884-1.71910.2451610.19443285344694
1.7191-1.75220.22651610.18893318347994
1.7522-1.78790.2211580.17773305346395
1.7879-1.82680.23851770.17583380355796
1.8268-1.86930.18191800.17383405358597
1.8693-1.9160.22821830.17453409359298
1.916-1.96780.19561980.16673475367398
1.9678-2.02570.19371760.16273408358499
2.0257-2.09110.21051750.16153494366999
2.0911-2.16580.17451910.15313443363499
2.1658-2.25250.19921720.15443461363399
2.2525-2.35490.20121830.1543491367499
2.3549-2.4790.19042010.15173464366599
2.479-2.63420.19631860.15653442362898
2.6342-2.83740.18691930.1573448364198
2.8374-3.12260.17461740.15633432360697
3.1226-3.57360.17112010.1523401360296
3.5736-4.49920.15261810.13643434361596
4.4992-27.56420.15681830.15643550373397
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)
10.4928-0.10910.03590.555-0.01270.50950.0382-0.12620.14340.08870.0458-0.0988-0.20060.3216-0.06580.1733-0.09110.01010.1737-0.06140.163413.03215.608432.8671
20.5709-0.049-0.02320.50040.02941.05950.04930.0814-0.0633-0.04830.0185-0.0986-0.01160.4284-0.03190.1282-0.03970.00220.2833-0.03510.153318.2282-2.736820.9185
30.64460.1694-0.38290.86440.80531.4427-0.00440.16440.04540.0034-0.0781-0.003-0.17220.12660.02250.2299-0.16750.03550.3757-0.01420.235422.507710.65214.5199
40.5378-0.0154-0.13190.43790.00730.42650.0250.02550.1340.01280.0564-0.0566-0.13940.3174-0.06660.1397-0.0740.00490.2176-0.0230.151713.29944.897522.3234
50.73530.1052-0.13190.63510.47441.75650.0028-0.01740.09450.03170.08670.0319-0.09860.0759-0.08550.1238-0.0290.00880.10350.00070.14661.31113.916428.1246
60.4727-0.16280.40790.8915-0.49781.25880.00790.1959-0.1238-0.15330.0752-0.01580.22990.2536-0.08170.17360.030.01010.3014-0.04260.178116.5232-9.941311.7212
73.2940.40091.3560.79530.17751.26220.03940.0701-0.2666-0.0857-0.0051-0.02590.24740.132-0.02080.16640.0313-0.00960.1113-0.02710.19068.9497-18.030724.1195
81.5505-0.756-0.56871.8530.14841.05920.0195-0.23250.08140.20810.0534-0.08750.0337-0.168-0.08830.14250.00860.01120.22180.04640.1343-16.6181-2.024242.6054
91.68010.5383-0.16851.75750.43221.22270.0133-0.3420.08620.19630.0706-0.055-0.0138-0.0144-0.05970.18210.02770.00180.2373-0.00280.1332-10.88192.930147.1707
100.7805-0.0081-0.02690.660.25550.6266-0.0291-0.20880.06490.0442-0.00340.1484-0.0358-0.42460.02230.13270.02740.01490.28510.04070.1763-26.4983-0.387134.9094
110.88020.15670.09780.5822-0.11470.42020.0250.09280.0024-0.01240.0167-0.027-0.0308-0.1177-0.05210.126-0.0229-0.00150.10150.03890.1187-12.7636-2.704219.1069
120.579-0.14530.01740.55090.11960.66920.0065-0.0098-0.0041-0.01350.08110.12470.0262-0.2688-0.00220.1242-0.0424-0.01940.11190.05440.1698-18.188-4.737925.0363
130.55460.060.10530.72020.04590.63980.04530.1279-0.1994-0.08420.12460.09260.2279-0.2165-0.060.1845-0.1686-0.04770.30590.06190.2115-25.7228-19.011619.6156
140.71460.59080.50.75780.95341.50970.1172-0.0883-0.10520.1607-0.0231-0.02210.2554-0.1830.05870.2677-0.1524-0.02740.37860.14520.2516-25.3347-2033.231
150.3229-0.16280.22080.38040.15770.39630.0598-0.0583-0.18890.00370.05510.14670.2408-0.19650.03640.2592-0.1448-0.06310.12180.12840.273-16.7315-22.646530.8665
160.9177-0.2995-0.09772.170.97641.4975-0.0297-0.07430.1097-0.01570.11350.0765-0.1722-0.2123-0.08440.1340.01820.01580.14610.04810.1447-17.49692.290731.4954
170.8229-0.2589-0.12891.32130.71681.03030.0311-0.0703-0.01690.04020.042-0.01130.0019-0.0226-0.06440.1273-0.01060.00370.08160.02020.1413-5.5631-3.90933.1489
180.5861-0.33050.10440.8415-0.30180.86330.08940.2024-0.1336-0.0778-0.02810.00270.2518-0.1627-0.07990.205-0.0762-0.03520.22540.02560.2172-17.7388-16.767813.5732
193.3221-0.1847-0.00020.4887-0.0431.39970.01030.36360.0287-0.05660.10990.101-0.0454-0.0118-0.12060.1478-0.0389-0.01530.18050.04690.1345-10.7939-1.98210.3143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 132 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 189 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 207 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 208 through 257 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 289 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 290 through 320 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 321 through 348 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 51 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 71 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 107 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 132 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 167 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 168 through 189 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 206 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 207 through 234 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 235 through 257 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 258 through 289 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 290 through 320 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 321 through 348 )B0

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