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- PDB-4ln5: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4ln5
TitleCrystal structure of a trap periplasmic solute binding protein from burkholderia ambifaria (Bamb_6123), TARGET EFI-510059, with bound glycerol and chloride ion
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / 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
Solute-binding protein Bamb_6123
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / 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
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 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_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)38,5084
Polymers38,3451
Non-polymers1633
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.098, 97.340, 58.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

21A-609-

HOH

31A-630-

HOH

41A-655-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 38344.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: AMMD / Gene: Bamb_6123 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B2F6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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

Crystal growTemperature: 298 K / pH: 8.5
Details: Protein (16.23 mg/ml, 10 mM HEPES pH 7.5, 150mM NaCl, 5% glycerol, 5 mM DTT), Reservoir (0.8 M Lithium Chloride, 0.1 M Tris pH 8.5, 32%(w/v) PEG 4000 (MCSG1 C9)), Cryoprotection (20% ...Details: Protein (16.23 mg/ml, 10 mM HEPES pH 7.5, 150mM NaCl, 5% glycerol, 5 mM DTT), Reservoir (0.8 M Lithium Chloride, 0.1 M Tris pH 8.5, 32%(w/v) PEG 4000 (MCSG1 C9)), Cryoprotection (20% Reservoir, 80% of 50% PEG3350), sitting drop vapor diffusion, temperature 298K

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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: Jul 2, 2013 / 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: 2.1→68.386 Å / Num. all: 16289 / Num. obs: 16289 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.216.80.6681.21601823410.668100
2.21-2.357.40.5261.51634722170.526100
2.35-2.517.40.38121542920850.38199.9
2.51-2.717.40.2932.61441919560.293100
2.71-2.977.40.1894.11327818020.189100
2.97-3.327.30.1256.11201716400.125100
3.32-3.837.20.08291043414520.082100
3.83-4.770.06610.6868012410.066100
4.7-6.646.90.06210.768299840.06299.9
6.64-58.1156.40.04912.136325710.04998.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFY

2pfy


Resolution: 2.1→48.67 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8553 / SU ML: 0.23 / σ(F): 0 / σ(I): 0 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 820 5.04 %RANDOM
Rwork0.1542 ---
all0.1574 16269 --
obs0.1574 16269 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.8 Å2 / Biso mean: 25.7937 Å2 / Biso min: 8.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 8 182 2526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072404
X-RAY DIFFRACTIONf_angle_d1.0313254
X-RAY DIFFRACTIONf_chiral_restr0.07356
X-RAY DIFFRACTIONf_plane_restr0.005426
X-RAY DIFFRACTIONf_dihedral_angle_d13.637901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.23160.2531430.182425282671100
2.2316-2.40390.27141470.176125292676100
2.4039-2.64580.24941240.180425652689100
2.6458-3.02860.2651500.171325322682100
3.0286-3.81550.21291280.145926052733100
3.8155-48.670.16641280.13112690281899
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)
10.16450.19750.06620.23950.02990.1878-0.09120.0941-0.328-0.1524-0.012-0.11270.2914-0.152-0.02190.1919-0.04270.00630.1583-0.02660.167911.603521.40473.1897
20.19050.1032-0.03290.0573-0.02020.0083-0.09230.21240.1012-0.1340.08550.0176-0.0993-0.02420.00080.14930.066-0.00210.1317-0.00790.09915.410235.5015-3.3892
30.057-0.0502-0.00810.03240.01060.0188-0.04060.07610.0729-0.0246-0.01770.0678-0.12270.033700.13290.013-0.03510.0859-0.01250.124414.383139.75376.0626
40.1333-0.22-0.04270.4055-0.08690.3496-0.0298-0.05830.1160.0932-0.0515-0.0428-0.06810.07660.00010.13120.01-0.01570.1180.00320.131322.952239.189414.2651
50.15090.03630.0260.0774-0.07970.0969-0.01750.20260.31320.1344-0.0491-0.12860.03590.190.00080.1405-0.0204-0.0240.20790.03910.166331.671242.86813.1041
60.05050.0008-0.01510.01160.01730.0189-0.08440.1874-0.137-0.1084-0.0968-0.10470.07210.0957-0.00130.15150.02420.00630.17340.04590.141733.708833.90336.339
70.13980.0565-0.05960.1772-0.26950.3066-0.0380.0690.0857-0.0145-0.0548-0.00440.01030.0646-0.0810.07160.0161-0.02260.1756-0.00730.122921.070633.59937.6527
80.15440.0073-0.22280.49980.15420.5799-0.0949-0.11840.05070.2261-0.01580.04170.2416-0.0417-0.25830.16740.0606-0.00450.10260.04160.141417.796723.825313.4113
90.1220.0555-0.09240.0749-0.10190.1796-0.0668-0.15830.0913-0.0146-0.1908-0.1425-0.25970.259-0.02020.2792-0.0311-0.11710.27390.00370.23932.780444.864618.8069
100.02240.0307-0.03870.0414-0.05120.0665-0.0342-0.04840.04660.1741-0.07040.1626-0.0907-0.19950.04340.36820.10210.05520.0139-0.1898-0.094912.931148.240822.0256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 82 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 106 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 173 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 201 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 216 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 217 through 249 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 284 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 311 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 312 through 328 )A0

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