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

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Basic information

Entry
Database: PDB / ID: 4pgp
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634, TARGET EFI-510120) WITH BOUND 3-INDOLE ACETIC ACID
ComponentsExtracellular solute-binding protein, family 7
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


organic substance transport / transmembrane transport / periplasmic space
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
1H-INDOL-3-YLACETIC ACID / Solute-binding protein Dde_0634
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 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
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
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 / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._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 / _software.classification / _struct_keywords.text
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Extracellular solute-binding protein, family 7
B: Extracellular solute-binding protein, family 7
C: Extracellular solute-binding protein, family 7
D: Extracellular solute-binding protein, family 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,2399
Polymers147,4764
Non-polymers7635
Water7,602422
1
A: Extracellular solute-binding protein, family 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0442
Polymers36,8691
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular solute-binding protein, family 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1063
Polymers36,8691
Non-polymers2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Extracellular solute-binding protein, family 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0442
Polymers36,8691
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Extracellular solute-binding protein, family 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0442
Polymers36,8691
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.286, 145.536, 97.919
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Extracellular solute-binding protein, family 7


Mass: 36869.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Strain: G20 / Gene: Dde_0634 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q315G1
#2: Chemical
ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID / Indole-3-acetic acid


Mass: 175.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9NO2 / Comment: hormone*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein (68.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3-INDOLE ACETIC ACID); Reservoir (0.2 M di-Ammonium Hydrogen Citrate pH 5.0, 20 %(w/v) PEG 3350); Cryoprotection (80% Reservoir + 20% Ethylene Glycol)

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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: Mar 21, 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: 2.25→43.46 Å / Num. obs: 61615 / % possible obs: 92.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.91 Å2 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.099 / Net I/σ(I): 3.3 / Num. measured all: 190054 / Scaling rejects: 41
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
2.25-2.3131.0311303143300.67592
10.31-43.463.20.0437.818145660.02879.7

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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: FOURIER SYNTHESIS / Resolution: 2.25→35.742 Å / FOM work R set: 0.7201 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2618 3129 5.09 %
Rwork0.2023 58368 -
obs0.2054 61497 92.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.78 Å2 / Biso mean: 38.33 Å2 / Biso min: 7.9 Å2
Refinement stepCycle: final / Resolution: 2.25→35.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 0 88 422 9970
Biso mean--26.23 34.62 -
Num. residues----1237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149747
X-RAY DIFFRACTIONf_angle_d1.43813267
X-RAY DIFFRACTIONf_chiral_restr0.0781479
X-RAY DIFFRACTIONf_plane_restr0.0081726
X-RAY DIFFRACTIONf_dihedral_angle_d14.833532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.28520.40621210.34262641276291
2.2852-2.32270.33321400.31322678281893
2.3227-2.36270.33411480.28492660280893
2.3627-2.40560.33891360.26672640277691
2.4056-2.45190.34071300.25992658278894
2.4519-2.50190.33731330.25682643277691
2.5019-2.55630.28911410.24442618275992
2.5563-2.61580.29621460.24362664281093
2.6158-2.68120.2981220.24292598272091
2.6812-2.75360.32921530.23712682283593
2.7536-2.83460.30881310.2312616274792
2.8346-2.92610.30761380.22352676281493
2.9261-3.03060.30331640.22122607277192
3.0306-3.15190.27051370.20942706284393
3.1519-3.29520.2781410.20932715285695
3.2952-3.46880.30691490.19662665281494
3.4688-3.6860.24941500.17842727287795
3.686-3.97020.2541380.1682699283794
3.9702-4.36910.19561390.1572710284994
4.3691-4.99990.19261690.14492665283493
4.9999-6.29370.20081550.17892634278991
6.2937-35.74630.22161480.17412466261485
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)
11.4026-0.8954-0.23033.0511-0.7890.37130.06730.1253-0.1962-0.1993-0.01680.23960.22390.0796-0.06640.53410.0095-0.03060.3439-0.00660.173819.3806-12.0206-54.655
22.0979-0.12160.70112.7919-0.43773.21010.07870.22990.0056-0.585-0.14-0.4941-0.11360.35190.07970.50930.00660.10410.4337-0.01330.252735.1763.1542-63.8261
33.5461.3347-0.61272.58-1.0141.2302-0.21640.0108-0.5437-0.52160.1558-0.07750.05860.05540.04790.46310.0162-0.01140.3206-0.03110.26924.9201-7.4713-56.2445
45.85171.5723-0.88773.0294-0.2211.92040.0221-0.9948-0.17790.1131-0.2472-0.2693-0.00910.24810.15060.44310.0957-0.03350.34040.07650.20427.2701-6.6313-45.2506
54.1157-0.50130.11082.6018-1.22481.4465-0.0642-0.13230.4553-0.13480.23370.1057-0.3917-0.1418-0.22470.49010.0040.01080.3073-0.03590.169518.879310.5602-59.3907
62.9298-0.7339-0.73793.42770.79541.3986-0.08010.1254-0.38270.25870.1727-0.43290.2396-0.0255-0.0340.1675-0.0075-0.02430.1903-00.496532.9641-35.8223-94.0458
71.55680.1510.31612.02130.76470.7036-0.03190.1952-0.3530.33970.1793-0.6307-0.05850.1204-0.08450.1321-0.0143-0.05180.2634-0.02220.493940.3874-20.4807-90.2014
82.134-0.0888-0.18631.33280.20031.87530.0764-0.14390.32240.19410.01640.2290.0697-0.1693-0.13950.1420.0194-0.00380.27640.04670.347519.6949-13.6224-83.9612
92.32490.293-0.51431.78621.35361.9728-0.15850.1681-0.3619-0.16690.2975-0.2836-0.05180.1086-0.09130.0747-0.0238-0.01140.24860.01110.412133.1533-24.862-97.7057
104.18880.5763-0.09481.73580.4780.66650.1605-0.02950.15980.03940.0563-0.16610.0355-0.0911-0.1840.1916-0.0365-0.00570.2230.05280.391636.3153-6.0844-87.6932
112.1063-1.9225-0.57813.9263-0.33790.6698-0.0933-0.12660.24920.0950.1207-0.2524-0.04070.0817-0.03140.5113-0.0022-0.00770.37490.00660.192439.305-35.1668-41.8991
122.6528-0.0536-0.04650.9057-0.43781.86810.33050.57140.1923-0.7719-0.188-0.392-0.0870.1466-0.1260.92140.03640.22040.55390.04780.448950.7567-40.6146-62.0934
133.1359-0.5681-0.21342.8412-0.67370.6789-0.0206-0.0042-0.1425-0.0730.09930.1655-0.0409-0.05640.01580.52210.00910.01540.27310.03420.2134.6982-38.7655-46.0749
141.684-0.63320.52221.6275-0.68292.2888-0.10440.201-0.1964-0.5052-0.1016-0.42890.05680.10220.27520.67440.00830.00550.4031-0.00340.284650.357-53.7089-49.1427
150.8088-0.5378-0.39742.76020.23621.0404-0.0327-0.13320.10410.14080.11520.0673-0.08330.1262-0.07510.1223-0.01510.01450.23080.04770.368441.67520.5531-92.1348
162.8777-0.2041-0.47852.27290.15462.6357-0.02770.10920.1609-1.035-0.1074-0.7599-0.08070.27260.12240.4846-0.02270.14580.26250.04230.287953.362417.0989-111.0467
171.8728-0.8612-1.04163.37930.2543.2921-0.18760.0991-0.0772-0.21450.06960.4183-0.0072-0.24110.15080.1571-0.0567-0.06050.22560.07060.422637.279217.1715-96.6134
181.8389-0.1250.2223.0373-1.26942.5933-0.0313-0.014-0.345-0.593-0.1702-0.36580.31470.25650.13910.28320.04730.04480.25590.03360.478752.22432.5621-98.5042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 149 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 218 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 251 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 288 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 289 through 339 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 92 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 149 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 229 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 230 through 287 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 288 through 339 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 32 through 149 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 150 through 230 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 231 through 287 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 288 through 339 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 32 through 157 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 158 through 226 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 227 through 287 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 288 through 339 )D0

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