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- PDB-4n17: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4n17
TitleCrystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, With bound beta-D-galacturonate
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


carbohydrate transport / 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
beta-D-galactopyranuronic acid / Solute-binding protein Bamb_6123
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Zhao, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Zhao, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / 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 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Non-polymer description
Revision 1.3Nov 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 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,2165
Polymers36,9061
Non-polymers3104
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.152, 101.369, 55.720
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-533-

HOH

21A-754-

HOH

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Components

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


Mass: 36906.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: ATCC BAA-244 / AMMD / Gene: Bamb_6123 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B2F6
#2: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid / D-Galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 1.84 Å3/Da / Density % sol: 33.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 59.1 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-galacturonic acid, reservoir: 0.2 M calcium acetate, 0.1 M MES, pH 6.0, 20% w/v PEG8000 (MCSG1 B6), cryoprotection: 4:1 50% w/v ...Details: 59.1 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-galacturonic acid, reservoir: 0.2 M calcium acetate, 0.1 M MES, pH 6.0, 20% w/v PEG8000 (MCSG1 B6), cryoprotection: 4:1 50% w/v PEG3350:reservoir, 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: Sep 17, 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: 1.5→100 Å / Num. all: 43587 / Num. obs: 43587 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 14.35 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Χ2: 0.995 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.534.40.58819740.738191.8
1.53-1.555.70.54620930.805196.5
1.55-1.586.50.53321801.0911100
1.58-1.627.90.44621550.9081100
1.62-1.657.90.38321690.8931100
1.65-1.697.90.32621820.9181100
1.69-1.7380.28421460.9631100
1.73-1.7880.25321831.081100
1.78-1.838.10.2221681.1711100
1.83-1.8980.20221861.4571100
1.89-1.968.40.17521761.4131100
1.96-2.048.50.14321871.3381100
2.04-2.138.60.11821911.2761100
2.13-2.248.80.10221891.2451100
2.24-2.388.90.08821861.1561100
2.38-2.5690.07322040.981100
2.56-2.8290.05822140.7981100
2.82-3.2390.04622170.6551100
3.23-4.078.90.04122590.5131100
4.07-1008.50.0423280.434198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LNM

4lnm


Resolution: 1.501→24.415 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8729 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 2137 5.02 %RANDOM
Rwork0.1703 ---
all0.1719 42548 --
obs0.1719 42548 97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.86 Å2 / Biso mean: 20.6846 Å2 / Biso min: 6.05 Å2
Refinement stepCycle: LAST / Resolution: 1.501→24.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 16 326 2659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152418
X-RAY DIFFRACTIONf_angle_d1.3383286
X-RAY DIFFRACTIONf_chiral_restr0.071362
X-RAY DIFFRACTIONf_plane_restr0.007429
X-RAY DIFFRACTIONf_dihedral_angle_d13.176893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.501-1.53560.2832780.29311730180862
1.5356-1.5740.29611430.25622511265493
1.574-1.61660.30151350.233927492884100
1.6166-1.66410.25241400.210727682908100
1.6641-1.71780.2231360.196727512887100
1.7178-1.77920.22211550.192227502905100
1.7792-1.85040.21931320.171327652897100
1.8504-1.93460.19681530.175527562909100
1.9346-2.03660.19051600.172227522912100
2.0366-2.16410.17371420.166227562898100
2.1641-2.33110.20451450.159527782923100
2.3311-2.56540.18261470.157427952942100
2.5654-2.93610.24181450.162828072952100
2.9361-3.69710.18781520.152828372989100
3.6971-24.41790.16981740.156529063080100
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)
11.77850.357-0.24830.82460.01120.8637-0.00210.09160.28320.0052-0.0514-0.1149-0.28370.1430.02180.0975-0.0199-0.01870.11060.05710.139434.967727.25493.3974
21.68520.70940.4150.84470.31250.7952-0.07940.10890.109-0.0351-0.017-0.2021-0.1660.20530.02740.1248-0.0494-0.01330.18540.05360.158635.640224.677-2.8012
30.79680.11060.10230.63160.1490.65190.02090.0226-0.02370.1475-0.0397-0.03230.21080.07810.01540.12840.0083-0.00130.0720.00050.075132.510711.439210.722
40.63590.1631-0.29930.5901-0.09630.4534-0.0251-0.0432-0.07760.412-0.15260.43620.2042-0.24580.01850.145-0.14860.23490.1087-0.03620.195614.0833.05297.6539
50.64620.24270.19290.8068-0.00130.614-0.16380.31870.0452-0.1380.06760.21740.0901-0.31510.06650.0749-0.05830.00050.1918-0.03550.121713.858714.66892.0803
61.37430.1412-0.12060.53030.24680.5118-0.1050.19140.02920.0717-0.00460.06110.1085-0.02570.03620.0699-0.01010.00840.1185-0.00030.077526.964915.6777.1716
72.22330.0631-0.15110.51350.03960.72610.03880.01320.11530.0266-0.06050.0434-0.09740.0410.02340.08220.0054-0.00940.0955-0.01680.10530.173825.623212.4729
80.9543-0.6515-0.01281.10980.31020.1322-0.1759-0.1961-0.08230.5331-0.01580.23290.5069-0.1117-0.08250.4966-0.01130.12380.2066-0.01140.179615.32094.929118.6734
91.4573-0.7618-0.07761.2529-0.56362.07210.1760.1456-0.1026-0.2539-0.09960.06590.16440.11120.06620.3125-0.0189-0.08470.12760.05790.11535.57681.482621.6581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 56 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 72 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 153 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 191 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 216 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 217 through 249 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 250 through 284 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 285 through 311 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 312 through 327 )A0

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