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

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Basic information

Entry
Database: PDB / ID: 4ovr
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM XANTHOBACTER AUTOTROPHICUS PY2, TARGET EFI-510329, WITH BOUND BETA-D-GALACTURONATE
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / STRUCTURAL GENOMICS / ENZYME FUNCTION INITIATIVE / EFI
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
beta-D-galactopyranuronic acid / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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
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
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Oct 14, 2015Group: Non-polymer description
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Dec 25, 2019Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / chem_comp / pdbx_audit_support
Item: _atom_site.occupancy / _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4286
Polymers72,9692
Non-polymers4594
Water13,637757
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7504
Polymers36,4851
Non-polymers2653
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)36,6792
Polymers36,4851
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.314, 111.362, 59.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

21A-578-

HOH

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36484.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: Py2 / Gene: Xaut_3368 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7IKQ4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: 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.: 2 / Source method: obtained synthetically / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 757 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsProtein was treated with TEV prior to crystallization, but was neither checked for cleavage nor ...Protein was treated with TEV prior to crystallization, but was neither checked for cleavage nor purified away from cleaved TAG prior to crystallization.

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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: 2.06 Å3/Da / Density % sol: 40.43 % / Description: Long plate shaped rods.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (29.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (00.8 M Lithium Chloride 0.1 M Tris pH 8.5 32 %(w/v) PEG 4000); Cryoprotection (80% of 50% Peg3350, 20% Reservoir)

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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 8, 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: 1.65→111.362 Å / Num. all: 72924 / Num. obs: 72924 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 15.74 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.116 / Rsym value: 0.096 / Net I/av σ(I): 6.649 / Net I/σ(I): 17.9 / Num. measured all: 991316
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
1.65-1.74120.8140.7451126449105020.230.8140.7453.599.9
1.74-1.8412.80.5330.4871.612765999540.1460.5330.4875.499.9
1.84-1.9713.40.3410.3112.512600493830.0920.3410.3118.3100
1.97-2.1313.90.2210.1983.912205887570.0590.2210.19812.8100
2.13-2.3314.30.1530.1345.711567380910.040.1530.13418.4100
2.33-2.6114.50.1270.107710624273300.0330.1270.10722.4100
2.61-3.0114.50.10.0818.89487965380.0260.10.08128.4100
3.01-3.6914.30.0760.06110.77889655340.020.0760.06138.3100
3.69-5.2214.10.0610.04514.36116943500.0160.0610.04547.4100
5.22-111.362130.0680.0416.23228724850.0180.0680.0442.897.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→31.501 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.9077 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1703 3673 5.04 %
Rwork0.1405 69168 -
obs0.142 72841 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.25 Å2 / Biso mean: 20.6961 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 28 757 5430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014799
X-RAY DIFFRACTIONf_angle_d1.2516500
X-RAY DIFFRACTIONf_chiral_restr0.072728
X-RAY DIFFRACTIONf_plane_restr0.007843
X-RAY DIFFRACTIONf_dihedral_angle_d13.311815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.67170.26351190.192926492768100
1.6717-1.69460.23951440.183626122756100
1.6946-1.71880.22121350.172526122747100
1.7188-1.74450.20491240.168226632787100
1.7445-1.77170.20651380.158926232761100
1.7717-1.80080.18011430.155226362779100
1.8008-1.83180.18421310.159526302761100
1.8318-1.86510.18791670.151326322799100
1.8651-1.9010.16571370.151626042741100
1.901-1.93980.19571620.146426342796100
1.9398-1.9820.19731550.14326252780100
1.982-2.02810.16551360.139426142750100
2.0281-2.07880.17031330.134526712804100
2.0788-2.1350.1831240.125626772801100
2.135-2.19780.16331380.119226422780100
2.1978-2.26870.14041490.122626452794100
2.2687-2.34980.16681410.124426502791100
2.3498-2.44380.16171480.129726452793100
2.4438-2.5550.17481270.129826892816100
2.555-2.68960.18271490.132626692818100
2.6896-2.8580.19371350.144627022837100
2.858-3.07850.15831440.146926712815100
3.0785-3.3880.17631440.151427062850100
3.388-3.87750.1561480.135627052853100
3.8775-4.88230.13961480.11927472895100
4.8823-31.50670.16081540.15762815296998
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)
10.75430.187-0.41320.1828-0.15591.5156-0.16830.19030.0272-0.20720.056-0.0114-0.12630.07290.11980.1624-0.037-0.00970.13580.01080.104513.968659.440742.4569
20.7444-0.2294-1.18470.20960.04973.1665-0.15030.27850.014-0.17640.0560.0323-0.1326-0.29290.08460.1443-0.0458-0.020.1738-0.00880.09987.900558.660442.8284
30.5557-0.27730.50760.4328-0.50311.12190.0171-0.0273-0.089-0.0731-0.00540.10530.0804-0.01390.00430.0928-0.00730.00330.0969-0.01290.10078.546449.004152.7636
40.23540.3477-0.10740.6795-0.02740.8581-0.03890.0143-0.1288-0.11120.0441-0.16620.08470.0074-0.02050.1015-0.00610.01010.1024-0.00630.136423.544647.084255.2723
50.74310.53080.3030.60360.3270.63240.1074-0.2441-0.05390.1618-0.0515-0.06970.0490.0078-0.04660.1211-0.0124-0.01220.1606-0.00340.088619.008156.706376.2941
61.3564-0.51511.32370.5272-0.38121.44250.0182-0.12640.23330.1349-0.0662-0.1532-0.1175-0.04850.04890.1381-0.02730.00450.14180.01070.1114.992849.39771.8845
70.89580.45310.21331.0657-0.04951.3239-0.0503-0.020.0205-0.07650.0380.0163-0.09-0.01170.05450.069-0.0077-0.00880.0701-0.00830.069215.854558.384160.7388
80.41940.55550.361.11050.66961.8115-0.07480.06380.0159-0.10210.0251-0.0751-0.03580.0830.03690.1596-0.04920.01070.13230.00810.105823.491259.686448.0367
90.42880.4984-0.06021.09370.12750.2642-0.0732-0.0853-0.0955-0.05170.1073-0.3394-0.03680.1703-0.00290.13-0.0197-0.03130.16480.00580.142227.029351.004272.1502
104.61281.9852-1.14232.3027-0.67921.2696-0.03710.46020.1866-0.12220.0983-0.50860.00490.0068-0.01690.15870.0261-0.03570.1151-0.00560.326728.192535.673658.3286
111.18290.09420.76360.9996-0.16891.4212-0.0077-0.24110.01830.0742-0.0063-0.0060.05070.01750.00240.10070.01110.0180.1379-0.01790.127136.489181.186256.7162
121.2612-0.70431.39841.5385-1.15122.0683-0.0096-0.35790.12660.1790.0676-0.0991-0.08210.0179-0.02930.13250.018-0.00960.1874-0.03970.100437.237387.680157.7664
131.0017-0.2275-0.36060.54140.18731.03410.0136-0.05310.1251-0.15050.0678-0.2261-0.15950.2049-0.06460.1249-0.02250.03140.1194-0.01210.166845.067184.031341.3972
140.42660.1694-0.06520.62850.17570.81150.0365-0.052-0.1734-0.08790.0587-0.2683-0.06080.1371-0.0830.1178-0.01280.01390.1179-0.01980.202745.491475.461142.2501
151.01450.67130.44980.46070.32070.5792-0.25870.45130.0331-0.47320.19160.0678-0.2451-0.02580.06940.3058-0.0659-0.00570.2480.0050.162134.149584.504225.0456
160.93110.25470.37660.59010.21041.4148-0.06810.05250.0588-0.08160.01340.0379-0.1081-0.00880.05830.1033-0.004-0.0020.077-0.01640.111633.019282.664739.5964
172.25920.23941.35680.55840.48171.7592-0.0211-0.1275-0.04060.0277-0.00040.00650.1029-0.1220.01490.1136-0.02040.00860.10110.00770.120235.71672.874450.1662
180.9160.48910.27860.5689-0.120.2881-0.00750.283-0.2185-0.2894-0.0011-0.1978-0.15890.05190.02420.2152-0.06580.05140.2597-0.06350.200137.538174.669824.4445
192.68231.1686-0.37815.1869-1.14982.4582-0.1498-0.1994-0.09880.21280.0193-0.2351-0.17730.07310.01080.18710.02170.12830.2474-0.02070.387355.67472.01733.3274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 54 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 71 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 96 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 152 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 153 through 172 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 190 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 191 through 248 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 249 through 283 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 284 through 307 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 308 through 323 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 54 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 55 through 71 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 112 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 113 through 152 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 153 through 190 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 191 through 248 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 249 through 283 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 284 through 307 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 308 through 324 )B0

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