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

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Basic information

Entry
Database: PDB / ID: 4pgn
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM DESULFOVIBRIO ALASKENSIS G20 (Dde_0634, TARGET EFI-510120) WITH BOUND INDOLE PYRUVATE
ComponentsExtracellular solute-binding protein, family 7
KeywordsTRANSPORT 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
3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID / Solute-binding protein Dde_0634
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Oct 14, 2015Group: Data collection
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: 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)148,66114
Polymers147,4764
Non-polymers1,18510
Water22,5011249
1
A: Extracellular solute-binding protein, family 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1964
Polymers36,8691
Non-polymers3273
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)37,1343
Polymers36,8691
Non-polymers2652
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)37,1964
Polymers36,8691
Non-polymers3273
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)37,1343
Polymers36,8691
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.122, 144.459, 95.466
Angle α, β, γ (deg.)90.000, 90.330, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer

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Components

#1: Protein
Extracellular solute-binding protein, family 7 / TRAP PERIPLASMIC SOLUTE BINDING PROTEIN


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-3IO / 3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID


Mass: 203.194 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H9NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1249 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
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), 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: 1.8→33.9 Å / Num. obs: 124994 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.066 / Net I/σ(I): 7.2 / Num. measured all: 470607 / Scaling rejects: 2
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
1.8-1.833.70.81.72286061320.4899.9
9.86-33.93.40.03515.721816420.02281.4

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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: 1.8→29.301 Å / FOM work R set: 0.8502 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 6275 5.03 %Random Selection
Rwork0.1568 118551 --
obs0.1589 124826 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.44 Å2 / Biso mean: 27.28 Å2 / Biso min: 8.17 Å2
Refinement stepCycle: final / Resolution: 1.8→29.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9509 0 134 1249 10892
Biso mean--20.66 37.21 -
Num. residues----1237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119826
X-RAY DIFFRACTIONf_angle_d1.2913356
X-RAY DIFFRACTIONf_chiral_restr0.0751482
X-RAY DIFFRACTIONf_plane_restr0.0071737
X-RAY DIFFRACTIONf_dihedral_angle_d13.633599
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 (%)
1.8-1.82050.30892100.262138674077100
1.8205-1.84190.27512240.247639634187100
1.8419-1.86430.2612400.23339224162100
1.8643-1.88790.29971830.231139354118100
1.8879-1.91280.25821830.219439954178100
1.9128-1.9390.24492170.209439304147100
1.939-1.96670.25942130.206539174130100
1.9667-1.9960.2452010.205339924193100
1.996-2.02720.25771880.189139764164100
2.0272-2.06040.22732230.187338954118100
2.0604-2.09590.24622180.176339984216100
2.0959-2.1340.21431920.166338934085100
2.134-2.17510.21892120.160240094221100
2.1751-2.21950.18511930.146139744167100
2.2195-2.26770.20912010.145539614162100
2.2677-2.32040.18892100.141239374147100
2.3204-2.37840.18171990.135140014200100
2.3784-2.44270.1722000.133539514151100
2.4427-2.51450.1982000.133939914191100
2.5145-2.59570.19122330.138538954128100
2.5957-2.68840.19822470.145539354182100
2.6884-2.79590.18931800.142139984178100
2.7959-2.92310.19332080.148839764184100
2.9231-3.0770.21322030.152639784181100
3.077-3.26960.19542220.154139484170100
3.2696-3.52160.1861830.140539954178100
3.5216-3.87530.14962410.13539644205100
3.8753-4.43440.15362220.122839424164100
4.4344-5.58060.14872170.136439954212100
5.5806-29.30470.20162120.18643818403095
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)
10.74710.49040.11781.6254-0.49510.9313-0.07620.11910.23830.06780.13360.2719-0.2034-0.061-0.04040.160.00380.01430.14170.05210.190418.586815.247452.4146
21.9593-0.4727-0.20381.3876-0.07910.8085-0.0630.11930.02630.18350.17140.64-0.1347-0.1686-0.07290.14550.02740.06660.16740.08510.294813.53159.797554.9455
31.7152-0.191-0.34351.1277-0.42361.45120.0278-0.1139-0.08730.236-0.012-0.1968-0.10410.1025-0.0180.1494-0.0126-0.03780.1532-0.00630.141233.2439-0.293365.2516
42.2185-0.48650.13761.0289-0.40770.799-0.00490.1289-0.0588-0.0256-0.0341-0.1982-0.01050.12310.03290.1072-0.00590.00220.1767-0.00790.126334.40311.871754.9639
51.22920.10040.45121.8913-0.75881.4749-0.04930.40790.2406-0.22090.10860.2805-0.1112-0.05520.00430.1446-0.0376-0.02410.190.09030.173520.874512.769546.2523
62.99350.7922-1.35480.5234-0.85961.36270.03460.4333-0.6007-0.03170.05-0.24550.2969-0.1284-0.13870.2265-0.02020.00410.1878-0.04230.338631.1051-13.290858.2894
72.4589-0.13970.13421.7767-0.29181.15740.0267-0.0912-0.07110.07990.10860.2338-0.04-0.0907-0.11760.1343-0.0380.03160.17850.00620.15588.1991-3.856259.3791
81.05140.32050.08681.44290.39261.5202-0.0358-0.13270.136-0.00750.0283-0.1041-0.18120.01320.00230.14680.03030.0010.1237-0.04330.149928.115440.108296.6689
90.89730.05240.04541.47040.46280.5353-0.0550.05080.0057-0.17010.0788-0.2579-0.07210.0445-0.02580.1396-0.01310.03830.1178-0.0290.116233.114927.522486.1452
101.91670.4885-0.08571.46790.32020.7681-0.08240.13380.0429-0.14950.194-0.3359-0.09460.0869-0.07120.1225-0.02740.04260.1361-0.0310.181935.787827.269488.2313
111.9570.60360.16921.30740.34921.5068-0.06040.047-0.213-0.25750.01580.1938-0.0577-0.13050.03510.134-0.0053-0.00780.1178-0.01620.165915.896117.084978.4321
121.83830.62380.05391.07370.31940.7771-0.0946-0.1424-0.0405-0.01460.08980.2734-0.0156-0.1361-0.0020.1058-0.00250.01480.16350.0180.168614.858119.610188.6386
131.6090.39490.42031.84720.34341.3919-0.0446-0.18640.05560.1760.0533-0.1441-0.1252-0.09240.02360.11140.02640.00950.1223-0.03720.110529.362830.889196.8522
141.4470.0238-0.50590.0667-0.15931.3221-0.0401-0.2535-0.1977-0.18230.23220.45580.4924-0.1070.36450.0961-0.07670.05760.18970.08080.441616.9625.499785.732
150.97480.40810.38691.41540.51851.22490.00340.0066-0.1434-0.08630.2135-0.3429-0.0880.2027-0.15760.134-0.00880.05190.1515-0.03570.202141.028313.39184.345
161.96910.23270.41791.1941-0.10671.2453-0.06830.1593-0.0235-0.11520.1490.17910.0855-0.028-0.08980.2308-0.0174-0.0130.18460.11240.26629.113631.398541.3527
170.71680.37250.68461.329-0.22412.6001-0.01540.2796-0.5854-0.21930.2-0.34660.23420.385-0.0830.25410.0270.01060.26010.01730.279843.440428.191537.9939
181.32760.3660.43721.4428-0.29620.9813-0.26270.34790.4757-0.12370.17090.1111-0.07690.37360.11850.1982-0.0548-0.0660.27250.16460.298241.766146.053939.4307
191.45760.11220.36561.0418-0.04931.307-0.0246-0.36520.02360.516-0.0385-0.07760.11890.18920.0380.35210.0175-0.06950.37440.07130.213848.70743.214159.3345
202.08750.67460.24541.7110.08711.7159-0.1440.08030.2738-0.06470.13230.44660.06870.0256-0.00830.2005-0.018-0.02440.18460.13970.295731.321239.782443.0772
210.9494-0.2106-0.37591.0864-0.53012.4842-0.27810.08350.49610.40210.0032-0.1571-0.25690.0470.17920.355-0.1127-0.12040.3920.06940.387851.495256.258852.6724
222.5864-0.3695-0.48761.35570.24351.3863-0.3580.03520.16570.02760.066-0.0075-0.1280.26960.02550.2393-0.0803-0.10440.35030.19860.452542.524858.275536.5778
231.60690.19290.15771.3631-0.18390.97260.00730.0599-0.0692-0.04090.06360.11450.06480.0235-0.05470.13830.01230.0020.08720.05780.119128.5118-23.141589.5902
240.73420.14321.14481.5182-0.1282.84690.12910.0517-0.2908-0.16330.0369-0.40470.30930.2507-0.0860.17060.02970.03480.14280.0180.218642.9351-26.296786.0892
250.68030.4830.17591.2906-0.1650.9277-0.03540.03670.09970.061-0.028-0.0721-0.05350.1690.05030.1305-0.00570.00420.14730.04060.132441.8126-7.150988.9442
260.9950.39170.58741.12650.1771.6659-0.00170.1021-0.0431-0.13510.0791-0.1452-0.11780.0606-0.01980.1239-0.00270.02720.10670.03150.103440.323-11.452485.7844
2710.1239-0.13640.3839-0.20171.9194-0.0554-0.1960.18760.438-0.0597-0.3105-0.26620.27410.05080.3751-0.0328-0.13550.3260.01650.190252.4158-7.2289108.8038
281.8638-0.14390.28320.5653-0.07461.63850.0537-0.0323-0.10830.2108-0.1204-0.16470.20070.36650.02160.30260.0273-0.09060.29410.06220.186750.3358-16.8586106.282
291.01980.21820.15830.4633-0.1571.7312-0.0302-0.2056-0.02030.3950.093-0.1075-0.03040.10060.01470.3080.0301-0.02770.20920.05470.106740.9382-11.6704108.2359
301.7580.6451.44431.5840.79362.26120.04430.1978-0.144-0.32120.0742-0.00680.11830.0246-0.07160.22230.0105-0.00790.12830.01920.111735.135-21.169478.0605
311.12790.11120.39541.2757-0.20682.08070.0504-0.22250.18350.14270.06970.25520.0866-0.3124-0.08410.15250.01080.03830.14240.070.134828.7748-12.112597.3202
321.3541-0.2213-0.21810.519-0.09170.0883-0.1895-0.06780.42560.35190.2908-0.4799-0.2938-0.0417-0.01690.6569-0.1127-0.05240.352-0.07710.342648.04161.8797110.4467
332.86230.64020.53771.0559-0.30575.0678-0.07290.02-0.21250.2762-0.2451-0.6137-0.0930.36780.09750.1497-0.0775-0.03650.20990.05380.320155.1597-0.833787.3462
343.3069-0.5024-0.64941.28690.19330.90.13320.04750.23190.00920.01280.037-0.1029-0.0248-0.05980.1363-0.00240.02270.16540.01040.226841.2944.157685.3113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 134 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 154 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 212 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 237 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 288 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 307 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 308 through 339 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 74 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 134 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 135 through 154 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 155 through 212 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 237 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 238 through 287 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 288 through 307 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 308 through 339 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 32 through 74 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 75 through 93 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 94 through 154 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 155 through 237 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 238 through 288 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 289 through 320 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 321 through 341 )C0
23X-RAY DIFFRACTION23chain 'D' and (resid 32 through 74 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 75 through 93 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 94 through 134 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 135 through 154 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 155 through 184 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 185 through 212 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 213 through 237 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 238 through 251 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 252 through 288 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 289 through 307 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 308 through 321 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 322 through 341 )D0

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