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

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Basic information

Entry
Database: PDB / ID: 4ovs
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFUROSPIRILLUM DELEYIANUM DSM 6946 (Sdel_0447), TARGET EFI-510309, WITH BOUND SUCCINATE
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
SUCCINIC ACID / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesSulfurospirillum deleyianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
GMGM093342 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
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords / struct_site / symmetry
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_site.details / _symmetry.Int_Tables_number
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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter, DctP subunit
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1435
Polymers75,8712
Non-polymers2723
Water9,818545
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0893
Polymers37,9361
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0542
Polymers37,9361
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.637, 49.146, 96.030
Angle α, β, γ (deg.)90.000, 109.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 37935.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurospirillum deleyianum (bacteria) / Strain: DSM 6946 / Gene: Sdel_0447 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D1AZL7
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.81 % / Description: Plate like crystal, tends to stack
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (29.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM SUCCINATE); Reservoir (0.2 M Potassium Sodium Tartrate, 20 %(w/v) PEG 3350); Cryoprotection (20% glycerol)

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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: Nov 26, 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: 1.8→90.617 Å / Num. all: 56917 / Num. obs: 56917 / % possible obs: 82.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 25.14 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.098 / Rsym value: 0.075 / Net I/av σ(I): 7.698 / Net I/σ(I): 13.2 / Num. measured all: 356000
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.93.51.2070.9280.81268936260.6211.2070.9281.236.7
1.9-2.013.90.6340.491.62156755440.3130.6340.492.359.5
2.01-2.154.50.3730.292.63341374610.1730.3730.294.184.1
2.15-2.326.40.2650.2193.45182581320.1040.2650.2196.998.5
2.32-2.557.40.1920.1614.65615876030.0710.1920.1619.9100
2.55-2.857.50.1370.1116.65174069070.050.1370.11113.8100
2.85-3.297.40.0960.0759.24559961320.0350.0960.07520.5100
3.29-4.027.30.070.054123784851890.0260.070.05428.9100
4.02-5.697.20.0650.048132923440480.0240.0650.04832.499.9
5.69-90.61770.0690.04413.81592722750.0250.0690.04431.699.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→41.565 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.7875 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 2880 5.09 %
Rwork0.1829 53684 -
obs0.1856 56564 82.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.72 Å2 / Biso mean: 37.9886 Å2 / Biso min: 15.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 17 545 5466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145051
X-RAY DIFFRACTIONf_angle_d1.3636814
X-RAY DIFFRACTIONf_chiral_restr0.08738
X-RAY DIFFRACTIONf_plane_restr0.008875
X-RAY DIFFRACTIONf_dihedral_angle_d14.8111892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82950.3498480.319990695429
1.8295-1.86110.306500.30831138118837
1.8611-1.89490.3372810.28581290137142
1.8949-1.93140.346660.26841584165051
1.9314-1.97080.34891000.26511780188058
1.9708-2.01360.28861070.25742069217667
2.0136-2.06050.28721110.24432390250177
2.0605-2.1120.30321420.23142646278886
2.112-2.16910.2811460.2172818296492
2.1691-2.23290.28131650.21723029319497
2.2329-2.3050.27461890.21433041323099
2.305-2.38740.28911880.20563043323199
2.3874-2.4830.27821620.19293057321999
2.483-2.59590.25891680.19523068323699
2.5959-2.73280.22361490.19453105325499
2.7328-2.9040.24431660.19883071323799
2.904-3.12810.26381870.19653054324199
3.1281-3.44280.23081760.17373070324699
3.4428-3.94060.18081620.14631153277100
3.9406-4.96340.1871540.133831903344100
4.9634-41.57560.18671630.16333220338399
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)
11.6612-0.0412-0.72821.13370.04041.520.0702-0.04520.11080.044-0.0739-0.1896-0.1870.10110.00830.2705-0.00490.02120.11410.00210.222454.880525.448186.0692
21.71380.2722-0.36430.618-0.10351.51910.05810.4337-0.0075-0.2229-0.05780.1053-0.1025-0.35890.02160.26770.0483-0.01080.2782-0.0440.226936.426218.715978.4259
31.12870.0173-0.13170.4828-0.14210.62680.12240.21810.1303-0.1607-0.07360.1225-0.4125-0.5842-0.05860.29030.1299-0.00910.3389-0.01080.269127.925327.793889.2749
42.02920.1729-0.31380.7980.23851.101-0.06260.2899-0.2149-0.3148-0.0336-0.1541-0.01590.03560.06320.29230.02770.06310.179-0.00870.2350.846817.582579.8692
52.0885-1.5827-1.29552.50981.44771.8120.0221-0.1434-0.12150.0496-0.0672-0.1456-0.11440.24360.06750.26030.02890.01060.2046-0.03230.219734.973816.3339102.4914
61.06520.43131.47891.6471-0.2362.5410.02670.408-0.0249-0.0535-0.17630.64020.065-0.7633-0.03990.1941-0.02760.01010.5484-0.0830.398219.442514.122391.7842
70.6433-0.20610.04580.7248-0.4560.6074-0.0270.3024-0.1289-0.1290.15370.09910.0358-0.5539-0.05790.35630.1101-0.15420.7994-0.19580.412625.948712.172269.7032
81.2418-0.31410.06671.0606-0.41582.0245-0.00230.0931-0.1025-0.1219-0.04320.20770.12640.00470.01680.3104-0.02030.02850.1316-0.0090.21768.289920.109439.8195
90.96330.0349-0.16010.67640.25821.9326-0.0595-0.0426-0.0731-0.09280.0313-0.2208-0.04230.81640.01570.2762-0.0050.03830.42180.04610.275488.814425.685347.3619
100.8635-0.24340.05670.8784-0.03090.7978-0.1213-0.2032-0.165-0.0045-0.1269-0.16730.42840.56360.17570.30920.11030.04570.33060.07190.247383.446217.066660.6995
111.28310.04680.63430.78280.112.2499-0.07030.2646-0.0336-0.295-0.0102-0.0305-0.31390.21940.10340.3369-0.01420.03080.20710.0150.207374.872528.220937.2564
120.6417-0.80020.54323.3974-1.56370.8152-0.04440.08250.097-0.0259-0.05780.0016-0.0709-0.02930.11130.36780.00860.02780.24460.04190.242673.375528.867265.4691
131.2447-0.186-0.4270.90690.19491.2797-0.0069-0.19560.21310.06440.045-0.3135-0.29141.1666-0.05060.3228-0.1261-0.050.72670.07650.380496.585332.655555.7287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 72 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 161 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 225 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 270 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 287 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 288 through 308 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 309 through 330 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 72 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 181 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 182 through 225 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 226 through 270 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 271 through 287 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 288 through 330 )B0

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