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- PDB-4mhf: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Entry
Database: PDB / ID: 4mhf
TitleCrystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Glucuronate, space group P21
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / 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 / carbohydrate transport / transmembrane transport / outer membrane-bounded periplasmic space / Solute-binding protein Bpro_3107
Function and homology information
Specimen sourcePolaromonas (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / 1.46 Å resolution
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
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. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 29, 2013 / Release: Sep 18, 2013
RevisionDateData content typeGroupProviderType
1.0Sep 18, 2013Structure modelrepositoryInitial release
1.1Feb 25, 2015Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,1113
Polyers36,7221
Non-polymers3882
Water8,485471
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)45.480, 45.960, 63.980
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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


Mass: 36722.359 Da / Num. of mol.: 1 / Source: (gene. exp.) Polaromonas (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_3107 / Plasmid name: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q128M1
#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical ChemComp-GCU / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 1.8 / Density percent sol: 31.84 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (> 50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Glucuronate, 5 mM DTT); Reservoir (2.0 M Ammonium Sulfate, 0.1 M Tris, pH 8.5(MCSG1 F10)); Cryoprotection (20% Diethylene Glycol, 80% of Reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Aug 23, 2013
RadiationMonochromator: GRAPHITE / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 8.31 Å2 / D resolution high: 1.46 Å / D resolution low: 63.409 Å / Number all: 41662 / Number obs: 41662 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.046 / Rsym value: 0.046 / NetI over sigmaI: 26.2 / Redundancy: 6.3 % / Percent possible obs: 92.6
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured allNumber unique allRsym valueRedundancyPercent possible all
0.1331.4601.5404.9003616857180.1336.30087.800
0.1021.5401.6406.2003469955200.1026.30089.000
0.0761.6401.7507.8003343252780.0766.30090.700
0.0591.7501.89010.3003156149720.0596.30091.900
0.0471.8902.07012.8002966946690.0476.40093.400
0.0442.0702.32013.3002724042890.0446.40094.700
0.0422.3202.67013.8002425338350.0426.30096.000
0.0352.6703.28015.9002081233090.0356.30097.300
0.0393.2804.63015.0001625726090.0396.20098.400
0.0394.63022.98014.500869414630.0395.90098.500

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Processing

Software
NameVersionClassificationContact authorContact author emailDateLanguageLocationType
SCALA3.3.20data scalingPhil R. Evanspre[at]mrc-lmb.cam.ac.uk2011/05/18Fortran_77http://www.ccp4.ac.uk/dist/html/scala.htmlother
PHENIX1.8.1_1168refinementPaul D. AdamsPDAdams[at]lbl.govC++http://www.phenix-online.org/package
PDB_EXTRACT3.11data extractionPDBdeposit[at]deposit.rcsb.orgApril 22, 2011C++http://sw-tools.pdb.org/apps/PDB_EXTRACT/package
MOSFLMdata reduction
AMoREphasing
RefineMethod to determine structure: FOURIER SYNTHESIS / Occupancy max: 1 / Occupancy min: 0.3 / Overall FOM work R set: 0.9374 / Overall SU ML: 0.09 / R Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Overall phase error: 12.3 / 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: 65.73 Å2 / B iso mean: 12.2561 Å2 / B iso min: 0 Å2
Least-squares processR factor R free: 0.1447 / R factor R work: 0.1173 / R factor obs: 0.1187 / Highest resolution: 1.46 Å / Lowest resolution: 21.582 Å / Number reflection R free: 2108 / Number reflection all: 41631 / Number reflection obs: 41631 / Percent reflection R free: 5.06 / Percent reflection obs: 92.18
Refine hist #LASTHighest resolution: 1.46 Å / Lowest resolution: 21.582 Å
Number of atoms included #LASTProtein: 2310 / Nucleic acid: 0 / Ligand: 26 / Solvent: 471 / Total: 2807
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082416
X-RAY DIFFRACTIONf_angle_d1.2493266
X-RAY DIFFRACTIONf_chiral_restr0.074371
X-RAY DIFFRACTIONf_plane_restr0.008419
X-RAY DIFFRACTIONf_dihedral_angle_d12.029920
Refine LS shell

Refine ID: X-RAY DIFFRACTION / Total number of bins used: 15

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.460.16040.13831.49911282440256887.0000
1.49910.18290.12431.53651172514263188.0000
1.53650.14300.11541.57811372539267688.0000
1.57810.14430.11311.62451382494263289.0000
1.62450.14180.11491.67691262558268490.0000
1.67690.16310.11521.73681492543269291.0000
1.73680.14930.11611.80631392607274691.0000
1.80630.14980.11361.88851462625277192.0000
1.88850.13830.11211.98801452620276593.0000
1.98800.14510.10612.11241562648280493.0000
2.11240.13250.10522.27541392716285594.0000
2.27540.13880.10862.50411392728286795.0000
2.50410.14380.11672.86571552765292096.0000
2.86570.14980.12143.60771642794295897.0000
3.60770.13550.133621.58391302932306298.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.2712-0.0288-0.15480.1720-0.09060.15780.00440.01490.0167-0.0313-0.03560.05420.0110-0.0770-0.00080.0413-0.01150.00440.0572-0.00740.04416.688519.954246.0672
20.2227-0.05680.19940.14780.06060.24310.0310-0.0177-0.05960.0140-0.0160-0.02560.0263-0.00380.00060.0342-0.00740.00090.03530.00630.043822.939716.355649.5991
30.0966-0.0256-0.00840.1800-0.19010.2063-0.03430.00450.05620.0810-0.0277-0.0419-0.11420.0332-0.00310.0601-0.0110-0.01060.0345-0.00230.038027.001735.363154.3022
40.04520.03330.04280.0491-0.03900.11600.02580.0791-0.01660.0114-0.08890.0094-0.07510.0551-0.00240.0579-0.0043-0.00110.03370.00650.049826.882634.865745.7745
50.2768-0.03730.09220.06330.07990.2222-0.02740.0084-0.0463-0.0679-0.01240.00170.0563-0.0208-0.00720.0429-0.01480.00420.0283-0.00540.034914.070616.465242.2632
60.0415-0.00330.06020.04410.02010.0485-0.02940.14440.1484-0.0913-0.1358-0.18450.00370.1758-0.07020.0654-0.00540.01310.10580.03590.129438.152233.304645.3070
70.09460.03790.04900.02060.04120.11170.08120.0468-0.08110.06310.0288-0.06330.12600.05290.00090.0658-0.0020-0.02030.06810.00450.093936.022312.775753.9085
Refine TLS group

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

IDRefine TLS IDSelection details
11CHAIN A AND (RESID 31:86 )
22CHAIN A AND (RESID 87:158 )
33CHAIN A AND (RESID 159:221 )
44CHAIN A AND (RESID 222:240 )
55CHAIN A AND (RESID 241:289 )
66CHAIN A AND (RESID 290:305 )
77CHAIN A AND (RESID 306:331 )

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