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- PDB-4pdd: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4pdd
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM POLAROMONAS SP JS666 (Bpro_0088, TARGET EFI-510167) BOUND TO D-ERYTHRONATE
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / 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
(2R,3R)-2,3,4-trihydroxybutanoic acid / FORMIC ACID / MALONIC ACID / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesPolaromonas sp. JS666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
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
DepositionApr 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 2.0Dec 25, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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
B: TRAP dicarboxylate transporter, DctP subunit
C: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,30618
Polymers99,9393
Non-polymers1,36715
Water18,5731031
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8537
Polymers33,3131
Non-polymers5406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7496
Polymers33,3131
Non-polymers4365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7035
Polymers33,3131
Non-polymers3904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.521, 126.647, 92.023
Angle α, β, γ (deg.)90.000, 113.210, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-579-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 33313.051 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Gene: Bpro_0088 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12HD7
#2: Chemical ChemComp-EAX / (2R,3R)-2,3,4-trihydroxybutanoic acid / erythronic acid


Mass: 136.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O5
#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1031 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (34.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-ERYTHRONATE); Reservoir (0.1 M Bis-Tris Propane pH 7, 60 %(v/v) tacsimate); Cryoprotection (100% Tascimate pH 7.0)

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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: Apr 9, 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: 1.7→31.59 Å / Num. obs: 101896 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.06 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.061 / Net I/σ(I): 6.1 / Num. measured all: 348728 / Scaling rejects: 99
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.7-1.733.30.671.41643750150.43699.7
9.31-31.593.20.04412.819416050.02992.5

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P9K

4p9k


Resolution: 1.7→28.426 Å / FOM work R set: 0.8886 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1725 5076 4.99 %Random Selection
Rwork0.1388 96644 --
obs0.1405 101720 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.46 Å2 / Biso mean: 23.78 Å2 / Biso min: 9 Å2
Refinement stepCycle: final / Resolution: 1.7→28.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 108 1031 8143
Biso mean--32.42 34.65 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017256
X-RAY DIFFRACTIONf_angle_d1.2489783
X-RAY DIFFRACTIONf_chiral_restr0.0731085
X-RAY DIFFRACTIONf_plane_restr0.0071285
X-RAY DIFFRACTIONf_dihedral_angle_d14.1362745
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 (%)
1.7-1.71930.26931730.23483170334399
1.7193-1.73950.25351630.215632383401100
1.7395-1.76080.24621740.21183205337999
1.7608-1.7830.2621570.20533203336099
1.783-1.80650.22851640.1993198336299
1.8065-1.83120.22841790.18631903369100
1.8312-1.85740.24881560.18563222337899
1.8574-1.88510.25581650.183132313396100
1.8851-1.91460.2291690.1783192336199
1.9146-1.9460.22621490.175732173366100
1.946-1.97950.21941680.159232193387100
1.9795-2.01550.17911830.1532263409100
2.0155-2.05420.18451720.144132313403100
2.0542-2.09620.17211770.143731743351100
2.0962-2.14170.16631750.13832213396100
2.1417-2.19150.20631510.132432313382100
2.1915-2.24630.16621890.128932063395100
2.2463-2.3070.17351800.132632293409100
2.307-2.37490.16021830.122432093392100
2.3749-2.45150.151470.122232433390100
2.4515-2.53910.17731760.128332273403100
2.5391-2.64060.17091740.133431863360100
2.6406-2.76070.18551750.13932573432100
2.7607-2.90610.16791650.145432183383100
2.9061-3.0880.1711690.137132623431100
3.088-3.32610.16051620.131332313393100
3.3261-3.66020.16071490.121932723421100
3.6602-4.18840.12921900.10332213411100
4.1884-5.27140.12121700.105532563426100
5.2714-28.430.16581720.15413259343199
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)
11.48670.8307-0.89261.5128-0.40461.0557-0.09510.4841-0.2281-0.18960.15240.05780.1805-0.089-0.06110.1955-0.0113-0.07270.2809-0.07830.1965-6.016523.935717.3983
22.13990.32820.45892.0659-1.51464.4530.01010.19360.08230.01250.12690.3855-0.3176-0.3239-0.11150.16190.022-0.02520.16050.00780.1838-3.632238.193423.3513
32.42560.2631-0.10571.292-0.1431.02780.06830.1253-0.0606-0.0442-0.00710.047-0.02280.128-0.0580.13540.0045-0.00940.1437-0.0090.08219.719634.695625.4447
43.16940.0789-1.60441.5474-0.41943.7243-0.01190.1466-0.4703-0.00990.0118-0.08810.24720.158-0.0230.16370.0107-0.03630.111-0.04890.155613.013725.634227.7691
50.6972-0.0687-0.24310.6348-0.26550.89520.0680.4443-0.0732-0.147-0.0866-0.0566-0.09180.0855-0.02560.1952-0.0003-0.00460.31810.00540.077515.218339.195214.0617
63.7381.1813-0.85761.5674-0.46151.55990.01780.16180.1987-0.08690.01070.0098-0.13380.0446-0.02410.17530.00780.00390.20520.00190.108615.415147.073919.8149
71.78810.5575-0.28790.25990.02381.5209-0.040.560.2273-0.11880.08620.0829-0.0581-0.0343-0.01910.22110.0038-0.02820.33660.03580.08447.944345.901111.2142
80.9981-0.68970.64521.0043-1.34831.9584-0.0070.5987-0.0491-0.40460.06610.12110.0654-0.16260.01040.2722-0.0157-0.03090.4913-0.02810.088413.259340.54087.375
91.25910.3121-0.58251.3044-0.92862.5809-0.02430.3845-0.4927-0.24140.13820.05460.2340.0892-0.00310.1917-0.015-0.0610.2808-0.1450.20283.436824.166418.5783
100.2447-0.12490.78361.0673-0.31722.9122-0.0090.4514-0.0642-0.1478-0.0858-0.0749-0.0285-0.00790.04310.1835-0.00250.03780.3506-0.01550.131424.107940.902416.4255
114.9107-0.57850.35818.59091.52194.98870.01550.3604-0.4193-0.1489-0.0865-0.02340.26220.19930.21770.13580.0227-0.01290.1833-0.02910.189525.424427.957928.9126
121.5019-0.03410.26781.48350.06720.70350.021-0.1862-0.08580.0787-0.0150.5141-0.0703-0.16150.00760.15210.00550.03430.15830.05180.3123-7.223535.901153.0212
132.1367-0.9970.95413.22-1.25511.8978-0.0984-0.26420.13010.1760.0154-0.0967-0.07970.00470.07590.14980.00980.0420.15660.01670.11316.004941.282358.5431
140.9234-0.66240.31391.6301-0.14970.29350.032-0.1206-0.1617-0.06310.06770.10470.0714-0.0222-0.08360.1488-0.00890.02610.14890.0760.19556.341922.571153.5056
153.1098-1.5450.17162.8475-0.22830.610.01310.1236-0.1693-0.0860.01520.10850.02850.0448-0.02140.1478-0.0101-0.00450.14240.05120.15949.818723.333244.4972
160.58810.01340.07890.94430.00580.86360.0285-0.1009-0.25460.00650.06390.31670.1115-0.1364-0.08060.1598-0.0226-0.01150.15460.0930.27930.97417.865749.6389
170.3029-0.13640.36843.9586-0.25140.4566-0.0468-0.2687-0.11190.20220.02590.29990.0218-0.11570.02450.15130.00640.08470.23840.0720.2593-6.251836.244660.5358
181.79311.0107-0.20641.53290.19990.63170.018-0.2015-0.33960.13910.0185-0.08290.0349-0.0439-0.02750.15640.0116-0.00390.13570.05730.188215.732622.078953.9043
194.55971.2329-2.24945.0666-0.70472.14830.0273-0.5375-0.06980.2386-0.06470.0889-0.12750.07760.00780.16070.00460.00780.2430.02670.151418.133738.788660.273
200.98190.28970.44450.8670.1453.1499-0.04750.15930.2411-0.1308-0.0050.0879-0.231-0.23110.06460.1610.039-0.01890.17670.0490.2231-8.222166.869926.9499
211.8341-0.10320.11680.85390.31081.5357-0.01780.04580.0192-0.01030.00620.03960.0312-0.08630.00220.1235-0.00330.00310.11710.01190.11432.266156.678337.3939
222.45631.21960.76673.2411.55052.3401-0.08630.19590.2089-0.23860.0653-0.1516-0.14480.16220.01960.137-0.01040.0130.12530.05040.131412.500660.733629.8933
231.24660.024-0.31510.94471.09141.615-0.0183-0.21060.25610.13650.0594-0.00910.16350.2352-0.05580.11770.0175-0.00720.1225-0.02910.15177.638465.859247.978
243.06990.06691.29742.10820.95012.8111-0.0481-0.29240.00110.10780.0521-0.07670.06940.08-0.01680.1330.00360.00190.1297-0.00610.10278.188957.106752.2376
251.2330.2071-0.28931.14140.14711.1555-0.0269-0.20120.140.08520.01160.114-0.0159-0.0428-0.00330.14780.01580.01010.1668-0.04710.1683-1.296663.494452.6116
262.7205-0.3555-1.56831.40610.72242.9636-0.0076-0.22840.38130.0821-0.01480.1885-0.1775-0.11220.01310.12270.0061-0.00080.1298-0.05560.21813.375370.375151.4998
271.4796-0.24120.97421.74760.52796.6164-0.00990.4282-0.0745-0.17140.00740.16180.3037-0.18770.00060.1356-0.0096-0.00310.2093-0.00880.1319-2.434655.855423.5251
281.56840.1988-0.09871.67521.89884.88650.03080.16480.4075-0.21710.0288-0.0522-0.5675-0.0742-0.07820.19030.0259-0.00940.12570.07890.27152.303672.55132.1722
292.1738-1.1871-0.4891.62070.23450.8284-0.1018-0.30850.37480.04750.1663-0.09430.00960.0612-0.06010.1521-0.0075-0.01130.1852-0.0470.18716.257164.69651.2575
304.2795-0.3169-0.91455.5105-2.35645.8793-0.150.33980.4881-0.08090.1768-0.1683-0.18920.1475-0.06330.1184-0.02140.00220.17870.04150.181624.002960.965935.3581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 71 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 88 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 119 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 142 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 170 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 171 through 190 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 191 through 223 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 224 through 241 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 242 through 291 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 292 through 320 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 321 through 334 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 33 through 119 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 120 through 142 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 143 through 170 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 171 through 190 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 191 through 242 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 243 through 291 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 292 through 320 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 321 through 334 )B0
20X-RAY DIFFRACTION20chain 'C' and (resid 33 through 71 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 72 through 119 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 120 through 142 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 143 through 170 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 171 through 190 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 191 through 223 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 224 through 241 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 242 through 256 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 257 through 291 )C0
29X-RAY DIFFRACTION29chain 'C' and (resid 292 through 320 )C0
30X-RAY DIFFRACTION30chain 'C' and (resid 321 through 334 )C0

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