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

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Entry
Database: PDB / ID: 4pfr
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (Rsph17029_3541, TARGET EFI-510203), APO OPEN PARTIALLY DISORDERED
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
D-MALATE / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 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 27, 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 / _software.name
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: TRAP dicarboxylate transporter, DctP subunit
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6044
Polymers75,3362
Non-polymers2682
Water32418
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8022
Polymers37,6681
Non-polymers1341
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)37,8022
Polymers37,6681
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.981, 94.981, 203.414
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsbiological unit is a monomer

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 37667.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17029 / Gene: Rsph17029_3541 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3PQL6
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (35.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM L-Gulonate); Reservoir (0.1 M Bis-Tris Propane pH 7, 60 %(v/v) tacsimate); Cryoprotection (80% Reservoir + 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: Feb 24, 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: 2.6→203.41 Å / Num. obs: 33491 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 56.94 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.037 / Net I/σ(I): 16.4 / Num. measured all: 195951 / 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
2.6-2.725.90.6522.42403440590.2999.9
9.01-203.414.50.05437.438688670.02794.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
Aimless0.1.27data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→52.32 Å / FOM work R set: 0.7851 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1688 5.06 %
Rwork0.216 31699 -
obs0.2181 33387 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.55 Å2 / Biso mean: 41.27 Å2 / Biso min: 12.2 Å2
Refinement stepCycle: final / Resolution: 2.6→52.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 22 18 4228
Biso mean--46.06 27.51 -
Num. residues----535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084294
X-RAY DIFFRACTIONf_angle_d1.1265839
X-RAY DIFFRACTIONf_chiral_restr0.074654
X-RAY DIFFRACTIONf_plane_restr0.005760
X-RAY DIFFRACTIONf_dihedral_angle_d14.9291582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.67650.35431370.303726152752100
2.6765-2.76290.36231290.277926052734100
2.7629-2.86170.31191390.257525892728100
2.8617-2.97620.28231370.250726332770100
2.9762-3.11170.31191500.247625942744100
3.1117-3.27570.28811530.239926172770100
3.2757-3.48090.27971310.220926242755100
3.4809-3.74960.24831460.201626272773100
3.7496-4.12680.23591520.18526472799100
4.1268-4.72360.21121360.183426692805100
4.7236-5.94990.24361530.200327062859100
5.9499-52.33090.25531250.22572773289897
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)
10.8019-0.4534-0.07121.15-0.21511.031-0.06790.098-0.0631-0.3145-0.07320.1377-0.07940.0478-0.12170.52680.1891-0.03610.16380.10280.264628.522430.772783.0112
21.43360.43560.18153.9136-0.16431.08020.00410.33990.1796-0.35520.2448-0.0863-0.06650.0917-0.21740.53090.11780.010.41160.01130.182435.100224.093177.601
30.42250.00150.11090.3597-0.0910.33110.00980.10620.19710.0947-0.03260.0542-0.2186-0.1442-0.02270.4160.02940.04310.1490.0090.182440.423622.05894.3694
40.8722-0.14210.29980.7654-0.24991.60730.0308-0.19080.01880.11020.05980.1745-0.1108-0.5666-0.12260.2443-0.07040.04320.24270.03380.216230.31124.3574102.3582
51.31240.2902-0.53461.1628-0.27871.5723-0.0873-0.04570.32660.07270.04260.1667-0.4752-0.1241-0.03350.47170.18430.0130.1903-0.01010.286633.470430.606190.1596
60.95060.12290.11070.6676-0.21910.8943-0.09280.073-0.13530.1209-0.03940.052-0.0567-0.52750.08020.3522-0.06110.05330.285-0.0440.164137.142611.6046107.9512
71.1081-0.039-0.34072.9206-0.07921.4999-0.0780.03320.1528-0.049-0.0238-0.19390.01210.0309-0.06670.3445-0.04660.02560.0327-0.00120.270950.838623.8048103.1779
80.8253-0.0242-0.06440.8935-0.07291.28930.05130.28030.1463-0.14650.3772-0.3274-0.00370.6811-0.1780.2837-0.1158-0.01610.4406-0.13510.43148.5601-11.248585.3951
93.15110.24160.87350.6393-0.2820.43650.01270.1732-0.0246-0.21130.526-0.20980.03630.3245-0.10070.3752-0.19760.11040.6265-0.20770.369748.914-13.021179.3538
100.36950.140.00220.4421-0.02830.0827-0.04740.0515-0.15720.0428-0.01810.10240.01230.00380.02690.1969-0.355-0.08290.12110.04730.254629.3555-22.334690.4324
111.8717-0.3413-1.52862.0612-0.68791.934-0.06950.0657-0.1402-0.0354-0.038-0.0070.0997-0.020.02980.3412-0.27770.11830.42050.03230.307632.4966-34.59484.5303
121.28410.474-0.16040.7797-0.03640.72820.03770.16830.0273-0.02520.1284-0.1326-0.09660.0822-0.06090.4756-0.20360.00070.3279-0.01040.204235.7475-21.285878.6373
130.38050.27350.34430.64050.44480.92140.01990.23550.0295-0.16290.201-0.04590.06940.1031-0.06470.4328-0.2431-0.00990.31420.02640.244634.9101-14.079179.5788
140.48230.7982-0.36421.6748-0.56720.62020.0364-0.0366-0.01070.0220.0227-0.1213-0.01790.06910.0570.1942-0.1621-0.03180.1894-0.11530.428245.3503-1.346891.8314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 53 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 79 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 150 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 231 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 279 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 280 through 313 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 328 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 82 through 133 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 134 through 145 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 146 through 188 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 189 through 202 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 203 through 255 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 256 through 311 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 312 through 328 )B0

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