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- PDB-4x8r: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Entry
Database: PDB / ID: 4x8r
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM Rhodobacter sphaeroides (Rsph17029_2138, TARGET EFI-510205) WITH BOUND Glucuronate
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsSOLUTE-BINDING PROTEIN / Solute-binding protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP/TeaA / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / TRAP dicarboxylate transporter, DctP subunit
Function and homology information
Specimen sourceRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.9 Å resolution
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM Rhodobacter sphaeroides (Rsph17029_2138, TARGET EFI-510205) WITH BOUND Glucuronate
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2014 / Release: Dec 24, 2014
RevisionDateData content typeGroupProviderType
1.0Dec 24, 2014Structure modelrepositoryInitial release
1.1Feb 4, 2015Structure modelDerived calculations

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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)75,6728
Polyers74,9042
Non-polymers7686
Water10,467581
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8364
Polyers37,4521
Non-polymers3843
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)37,8364
Polyers37,4521
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)116.800, 116.800, 111.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP 42 21 2
Detailsbiological unit is a Monomer

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Components

#1: Protein/peptide TRAP dicarboxylate transporter, DctP subunit


Mass: 37451.980 Da / Num. of mol.: 2
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17029 / ATH 2.4.9) (bacteria)
Strain: ATCC 17029 / ATH 2.4.9 / Gene: Rsph17029_2138 / Plasmid name: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3PLM5
#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Formula: PO4 / Phosphate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Formula: H2O / Water

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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: 2.55 / Density percent sol: 51.73 %
Crystal growTemp: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein (30.12 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Glucuronate); Reservoir (MCSG 1, F7, 0.1 M Sodium/Potassium phosphate pH 5.6

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Details: MIRRORS / Detector: CCD / Collection date: Nov 12, 2014
RadiationMonochromator: GRAPHITE / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 15.31 Å2 / D resolution high: 1.7 Å / D resolution low: 5 Å / Number obs: 84879 / Rmerge I obs: 0.141 / Chi squared: 0.984 / NetI over av sigmaI: 16.827 / NetI over sigmaI: 5.5 / Number measured all: 1314798 / Redundancy: 15.5 % / Percent possible obs: 99.1
Reflection shell

Diffraction ID: 1 / Rejects: _

Highest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible allRmerge I obs
1.7001.73035250.91212.50083.300
1.7301.76042080.91814.300100.000
1.7601.79042190.94114.700100.000
1.7901.83042190.94414.900100.000
1.8301.87042310.96515.000100.000
1.8701.91042250.99415.100100.000
1.9101.96042311.01915.300100.0000.765
1.9602.02042480.99015.400100.0000.836
2.0202.07042430.96915.500100.0000.592
2.0702.14042440.96715.600100.0000.460
2.1402.22042620.96815.600100.0000.405
2.2202.31042211.04015.800100.0000.285
2.3102.41042720.91315.900100.0000.256
2.4102.54042920.87816.000100.0000.198
2.5402.70042890.84016.300100.0000.169
2.7002.91042910.87016.500100.0000.139
2.9103.20043221.29016.500100.0000.140
3.2003.66043411.67216.400100.0000.130
3.6604.61043980.91016.300100.0000.075
4.61050.00045980.62915.50099.2000.056

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefineOverall SU ML: 0.16 / Cross valid method: FREE R-VALUE / Sigma F: 1.35 / Overall phase error: 18.43 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 107.18 Å2 / B iso mean: 22.217 Å2 / B iso min: 3.32 Å2
Least-squares processR factor R free: 0.2013 / R factor R work: 0.1566 / R factor obs: 0.1587 / Highest resolution: 1.9 Å / Lowest resolution: 25.434 Å / Number reflection R free: 2951 / Number reflection R work: 58156 / Number reflection obs: 61107 / Percent reflection R free: 4.83 / Percent reflection obs: 99.53
Refine hist #finalHighest resolution: 1.9 Å / Lowest resolution: 25.434 Å / B iso mean ligand: 29.81 / B iso mean solvent: 32.43 / Number residues total: 608
Number of atoms included #finalProtein: 4804 / Nucleic acid: 0 / Ligand: 64 / Solvent: 589 / Total: 5457
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114964
X-RAY DIFFRACTIONf_angle_d1.2646724
X-RAY DIFFRACTIONf_chiral_restr0.051732
X-RAY DIFFRACTIONf_plane_restr0.006882
X-RAY DIFFRACTIONf_dihedral_angle_d14.8981852
Refine LS shell

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

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.90000.25670.24701.93121382576271494.0000
1.93120.26230.22111.96451392670280998.0000
1.96450.24160.19522.00021242734285899.0000
2.00020.22170.17092.038615227092861100.0000
2.03860.22630.16062.080214327402883100.0000
2.08020.18390.15292.125416227412903100.0000
2.12540.22040.15412.174815727182875100.0000
2.17480.22500.16472.229213427372871100.0000
2.22920.26710.20252.289415727552912100.0000
2.28940.18250.15922.356813627492885100.0000
2.35680.18190.13672.432814727692916100.0000
2.43280.18580.13032.519613827592897100.0000
2.51960.19710.13632.620413027752905100.0000
2.62040.19760.14272.739611727952912100.0000
2.73960.17980.15082.883811727932910100.0000
2.88380.22210.15873.064214828002948100.0000
3.06420.22330.16533.300313928062945100.0000
3.30030.19650.14723.631613528072942100.0000
3.63160.17880.13494.155114028452985100.0000
4.15510.14190.12095.227512228883010100.0000
5.22750.18790.177125.436417629903166100.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.0131-0.00370.00500.0237-0.03140.04220.0045-0.00960.00900.0306-0.01410.0054-0.01370.0199-0.02480.1276-0.02080.06060.0504-0.00780.06509.559446.711252.5641
20.00170.00190.00130.00220.00150.00130.0015-0.00100.00350.0021-0.00020.0031-0.00540.00760.00500.0710-0.02770.03720.07960.02780.061715.541944.109237.5793
30.02650.0106-0.01110.01550.01960.05940.0095-0.00760.00190.01110.00880.0060-0.00450.04050.04570.04740.01650.03230.05570.02130.041513.776227.864142.9901
40.00600.0143-0.01180.0470-0.02590.0209-0.01080.03780.0131-0.03350.05160.06240.0118-0.02080.0699-0.0118-0.04280.02950.04850.07490.03844.128232.683631.5342
50.00710.0011-0.00990.0234-0.01350.01880.00640.00160.00000.0377-0.01490.0297-0.0153-0.0039-0.01150.0615-0.00410.04390.07260.01550.06262.433136.145450.5717
60.00540.00090.00170.00120.00380.0213-0.00400.0088-0.0046-0.00290.02220.00910.0398-0.00660.01180.1203-0.00270.03740.09810.00420.16471.050119.142729.3229
70.00100.0010-0.00020.0012-0.00020.00000.00590.0035-0.00570.01280.00020.00240.00930.00830.00000.18400.11200.02250.17500.05070.174816.288614.715441.7607
80.00070.00040.00100.0005-0.00180.0122-0.00170.01260.0090-0.0100-0.00240.00490.0036-0.0049-0.01670.0417-0.0169-0.02740.08040.04610.060611.963552.44518.0857
90.00110.00020.00040.00300.00180.0058-0.01140.00920.0034-0.00790.00480.01690.0122-0.0101-0.00930.0479-0.0369-0.01010.08500.03870.062911.304446.202914.8416
100.00060.00020.00090.00240.00250.00370.00290.0178-0.0034-0.0179-0.0073-0.01520.03930.01420.00830.04790.00480.00640.07850.05100.063729.235444.130414.6083
110.00370.0047-0.00920.0086-0.00660.02510.0205-0.04950.01050.0323-0.0278-0.0216-0.01610.04960.00450.0442-0.0614-0.00450.07660.04790.026427.369753.520627.1193
120.00200.0034-0.00500.0043-0.00740.0104-0.01560.02310.02100.0009-0.0107-0.0159-0.00040.0211-0.03480.0848-0.0364-0.03330.07950.05760.065922.314557.22328.6790
130.0008-0.0007-0.00070.00040.00020.0010-0.0069-0.0011-0.00350.0070-0.0094-0.0083-0.01490.0378-0.00040.0852-0.0132-0.00570.14330.06380.161441.161954.814828.1837
140.00160.0018-0.00040.00250.00000.00280.00830.0079-0.0040-0.00320.0022-0.00460.00110.00390.00230.09950.06990.02920.18140.06020.162042.088639.988414.1525
Refine TLS group

Beg auth seq ID: _ / End auth seq ID: _ / Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDEnd auth asym IDRefine TLS IDSelection details
1AA1chain 'A' and (resid 22 through 63 )
2AA2chain 'A' and (resid 64 through 80 )
3AA3chain 'A' and (resid 81 through 134 )
4AA4chain 'A' and (resid 135 through 248 )
5AA5chain 'A' and (resid 249 through 284 )
6AA6chain 'A' and (resid 285 through 308 )
7AA7chain 'A' and (resid 309 through 325 )
8BB8chain 'B' and (resid 22 through 53 )
9BB9chain 'B' and (resid 54 through 79 )
10BB10chain 'B' and (resid 80 through 134 )
11BB11chain 'B' and (resid 135 through 248 )
12BB12chain 'B' and (resid 249 through 284 )
13BB13chain 'B' and (resid 285 through 308 )
14BB14chain 'B' and (resid 309 through 325 )

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