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- PDB-4p1l: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4p1l
TitleCrystal structure of a trap periplasmic solute binding protein from chromohalobacter salexigens dsm 3043 (csal_2479), target EFI-510085, with bound d-glucuronate, spg i213
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT 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 / carbohydrate binding
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-glucopyranuronic acid / Solute-binding protein Csal_2479
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. ...Vetting, M.W. / Al Obaidi, N.F. / 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
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Dec 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
Revision 1.8Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)74,95310
Polymers73,9932
Non-polymers9618
Water10,647591
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3834
Polymers36,9961
Non-polymers3863
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)37,5716
Polymers36,9961
Non-polymers5745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.120, 158.120, 158.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-403-

SO4

21B-403-

SO4

31B-404-

SO4

41B-404-

SO4

51A-567-

HOH

61A-665-

HOH

71B-503-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36996.258 Da / Num. of mol.: 2 / Fragment: TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_2479 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1QUN2
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10
Details: Protein (35.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Glucuronate); Reservoir (0.2M Lithium Sulfate 0.1 M CAPS pH 10.5 2.0 M Ammonium Sulfate ); Cryoprotection (20% glycerol + Reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→111.808 Å / Num. all: 71263 / Num. obs: 71263 / % possible obs: 99.1 % / Redundancy: 19.2 % / Biso Wilson estimate: 16.26 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.106 / Rsym value: 0.103 / Net I/av σ(I): 6.416 / Net I/σ(I): 20.5 / Num. measured all: 1370709
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.799.10.631.28871497600.2130.63393.9
1.79-1.9170.4941.616821199050.1220.4946100
1.9-2.03210.3442.219472892790.0770.3449.7100
2.03-2.1921.30.2273.418445586460.050.22714.2100
2.19-2.421.60.1714.317284080090.0380.17119.3100
2.4-2.6921.80.1275.615724472190.0280.12724.4100
2.69-3.121.90.0897.714042263980.0190.08932.7100
3.1-3.822.10.061111971154230.0130.0647.3100
3.8-5.3822.10.04813.39355442400.010.04856.5100
5.38-42.25921.30.03317.75083023840.0070.03350.599.8

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementResolution: 1.7→35.357 Å / FOM work R set: 0.9132 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 3605 5.06 %
Rwork0.1428 67630 -
obs0.1447 71235 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.33 Å2 / Biso mean: 23.59 Å2 / Biso min: 8.48 Å2
Refinement stepCycle: final / Resolution: 1.7→35.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 57 598 5378
Biso mean--22.01 32.66 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114920
X-RAY DIFFRACTIONf_angle_d1.2286690
X-RAY DIFFRACTIONf_chiral_restr0.071705
X-RAY DIFFRACTIONf_plane_restr0.007895
X-RAY DIFFRACTIONf_dihedral_angle_d13.4981826
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 (%)
1.7001-1.72250.27991160.26292312242889
1.7225-1.74610.27641270.24942438256593
1.7461-1.7710.26151290.23392506263596
1.771-1.79750.2431320.20842543267598
1.7975-1.82550.22761450.194326002745100
1.8255-1.85550.23531440.185425972741100
1.8555-1.88750.22221500.177825952745100
1.8875-1.92180.22511330.165926612794100
1.9218-1.95870.20431550.154325792734100
1.9587-1.99870.18391740.155125632737100
1.9987-2.04220.19681390.143326062745100
2.0422-2.08970.18211220.146526692791100
2.0897-2.14190.18861360.134526072743100
2.1419-2.19980.20081340.132325932727100
2.1998-2.26460.19661350.128226372772100
2.2646-2.33760.15681410.119626152756100
2.3376-2.42120.16581320.11726432775100
2.4212-2.51810.15981540.122226142768100
2.5181-2.63270.18011420.123126272769100
2.6327-2.77140.17241390.129726062745100
2.7714-2.9450.15891440.136326462790100
2.945-3.17220.15271280.140726432771100
3.1722-3.49120.17951350.13326682803100
3.4912-3.99580.16081340.122526652799100
3.9958-5.03190.14091440.114426492793100
5.0319-35.36430.18511410.16362748288999
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)
10.8255-0.0082-0.2011.31740.51790.7776-0.032-0.130.11360.12910.03390.0531-0.01490.0385-0.01190.174-0.01350.03090.1586-0.02960.164161.326368.047510.4
21.6749-0.1004-0.70381.58420.33921.4621-0.0447-0.0634-0.105-0.0171-0.00510.05280.04230.06670.01590.1687-0.01690.02990.1533-0.00050.179866.047349.57615.0705
30.47270.0263-0.31390.99140.0520.79310.0067-0.079-0.0448-0.03260.0133-0.2363-0.06760.2966-0.01430.1356-0.04890.03790.2002-0.0320.167873.081458.13960.1994
41.1143-0.1759-0.55171.46440.57972.2376-0.02340.00140.2494-0.07440.03590.128-0.2508-0.14340.02410.2029-0.01770.01750.1282-0.02360.209159.50976.46418.1452
50.3059-0.0587-0.28420.4746-0.26910.81960.02430.0633-0.1293-0.09190.06080.0156-0.0173-0.0121-0.06820.1735-0.05490.02270.1653-0.01660.143458.28349.678-1.5531
61.4768-0.22640.1512.1862-1.38362.1271-0.0390.0405-0.0729-0.0002-0.01240.25550.1152-0.2904-0.02060.1627-0.03210.0350.174-0.01160.231244.912555.36277.282
70.7890.22250.34770.70980.34330.726-0.0392-0.3040.16160.2628-0.2385-0.0416-0.14510.02330.07380.2269-0.1365-0.07190.26150.00450.180755.908941.275645.0583
80.40350.1193-0.0950.5112-0.12691.1334-0.0279-0.06990.0419-0.0188-0.194-0.1382-0.09640.41310.07040.1088-0.0671-0.02760.22480.07870.211262.193236.102528.2342
90.58270.466-0.0240.7264-0.34440.95650.0479-0.02480.0578-0.0284-0.14190.0666-0.01090.00960.05650.0783-0.01310.01230.0824-0.00890.137347.944933.339422.2016
101.13410.42490.23341.10080.29620.91680.02-0.2181-0.05970.1652-0.1547-0.26490.03110.2699-0.11280.171-0.1285-0.0830.2890.090.178361.997434.257742.6669
110.45230.642-0.04310.9821-0.23660.30950.01570.0201-0.0831-0.0375-0.0929-0.14170.05650.09330.03710.14280.01030.05180.13530.0270.19259.078329.46214.5709
120.22270.0294-0.01850.5186-0.10440.4102-0.0778-0.0185-0.0486-0.03-0.02-0.2179-0.05740.37580.03690.1137-0.05470.01890.40460.15120.344973.937137.420819.9736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 171 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 172 through 191 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 243 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 292 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 293 through 320 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 321 through 336 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 88 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 89 through 171 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 172 through 243 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 244 through 292 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 293 through 320 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 321 through 335 )B0

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