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- PDB-4mij: Crystal structure of a Trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4mij
TitleCrystal structure of a Trap periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Galacturonate, space group P21
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


carbohydrate transport / 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
alpha-D-galactopyranuronic acid / beta-D-galactopyranuronic acid / Solute-binding protein Bpro_3107
Similarity search - Component
Biological speciesPolaromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
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. ...Vetting, 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. ...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
DepositionAug 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2087
Polymers36,6511
Non-polymers5576
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.534, 46.140, 63.897
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36651.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_3107 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q128M1

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Sugars , 2 types, 2 molecules

#4: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#5: Sugar ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 506 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 1.82 Å3/Da / Density % sol: 32.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Galacturonate, 5 mM DTT); Reservoir (0.8 M Lithium Chloride, 0.1 M Tris, pH 8.5, 32 %(w/v) PEG 4000, (MCSG1 C9)); Cryoprotection (20% Ethylene ...Details: Protein (50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Galacturonate, 5 mM DTT); Reservoir (0.8 M Lithium Chloride, 0.1 M Tris, pH 8.5, 32 %(w/v) PEG 4000, (MCSG1 C9)); Cryoprotection (20% Ethylene Glycol, 80% of Reservoir), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Jul 23, 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: 1.1→63.341 Å / Num. all: 104054 / Num. obs: 104054 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 7.83 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.1-1.162.80.2992.236527130160.29984
1.16-1.233.50.232.851760146650.23100
1.23-1.313.60.1743.949881137530.174100
1.31-1.423.70.1394.847110128630.139100
1.42-1.563.70.16.743697118180.1100
1.56-1.743.70.0798.139966107150.079100
1.74-2.013.80.0787.53563794860.078100
2.01-2.463.80.05510.43036280280.055100
2.46-3.483.80.03714.32364662420.037100
3.48-34.6653.60.03316.41264334680.03399.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LN5

4ln5


Resolution: 1.1→34.665 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.9224 / SU ML: 0.09 / σ(F): 0 / σ(I): 0 / Phase error: 14.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1516 5187 4.99 %RANDOM
Rwork0.138 ---
obs0.1387 104014 97.62 %-
all-104014 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.16 Å2 / Biso mean: 13.8665 Å2 / Biso min: 5.22 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 33 502 2854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082484
X-RAY DIFFRACTIONf_angle_d1.2873366
X-RAY DIFFRACTIONf_chiral_restr0.077380
X-RAY DIFFRACTIONf_plane_restr0.008437
X-RAY DIFFRACTIONf_dihedral_angle_d12.126952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11250.27571240.25952356248070
1.1125-1.12560.28161250.242567269277
1.1256-1.13930.23951420.22922887302985
1.1393-1.15370.24211500.21583261341197
1.1537-1.16890.20081790.191633413520100
1.1689-1.18490.17651890.174833713560100
1.1849-1.20190.17511900.170433353525100
1.2019-1.21980.18661990.170433263525100
1.2198-1.23890.20981610.170833663527100
1.2389-1.25920.19251680.16833563524100
1.2592-1.28090.15371430.159734123555100
1.2809-1.30420.1571910.152133593550100
1.3042-1.32930.13791620.148233573519100
1.3293-1.35640.17511920.148333783570100
1.3564-1.38590.14891820.141533763558100
1.3859-1.41810.15431720.136733403512100
1.4181-1.45360.12861840.136433573541100
1.4536-1.49290.15041580.127534123570100
1.4929-1.53680.14841830.125433593542100
1.5368-1.58640.13821760.122933663542100
1.5864-1.64310.12871830.121433723555100
1.6431-1.70890.1351660.123133953561100
1.7089-1.78670.14111730.127233583531100
1.7867-1.88090.14181950.127833653560100
1.8809-1.99870.1381980.130433863584100
1.9987-2.1530.13971920.121533633555100
2.153-2.36970.12481640.115934153579100
2.3697-2.71240.15331830.127734123595100
2.7124-3.41690.14761870.129934013588100
3.4169-34.68260.14921760.13553478365499
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)
10.71670.2536-0.26070.7532-0.14950.36610.00480.01160.02260.0022-0.01240.0975-0.0054-0.05610.00860.08170.00010.00540.0946-0.00390.09556.772919.974445.9886
20.4757-0.01550.26560.32340.0540.5796-0.0141-0.0255-0.0120.0232-0.0114-0.0229-0.01480.02520.02520.0674-0.00390.00020.0730.00390.070625.12920.876950.67
30.48370.1420.14220.3928-0.05220.4581-0.0259-0.0090.04290.0432-0.0019-0.0008-0.0804-0.00170.02720.07760.00390.00230.0621-0.00250.060122.464530.019851.6819
40.8160.654-0.0771.4532-0.14420.4078-0.02370.0296-0.0334-0.0657-0.0109-0.01410.0308-0.00010.04090.0838-0.0002-0.00160.0865-0.00340.071316.400319.836637.6951
51.5976-1.74611.36651.9002-1.47271.15570.0310.29590.2089-0.132-0.2457-0.22960.0110.29390.18380.113-0.0061-0.00040.16740.03070.160938.335233.18745.1266
61.00470.1635-0.1631.2191-0.01991.0560.03340.0455-0.09240.01260.0404-0.04520.1479-0.0105-0.06490.08850.0015-0.01670.10810.00680.113836.014812.62352.9633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 31:86 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 87:178 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 179:254 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 255:289 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 290:305 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 306:332 )A0

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