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- PDB-4p3l: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4p3l
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CHROMOHALOBACTER SALEXIGENS DSM 3043 (Csal_2479), TARGET EFI-510085, WITH BOUND GLUCURONATE, SPG P6122
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 / 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 / SYNCHROTRON / Resolution: 1.8 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
DepositionMar 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Data collection
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _entity.src_method ..._citation.journal_id_CSD / _entity.src_method / _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 / _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 / entity ...chem_comp / 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 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2614
Polymers36,9961
Non-polymers2653
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.657, 160.657, 58.117
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit / TRAP PERIPLASMIC SOLUTE BINDING PROTEIN


Mass: 36996.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / Gene: Csal_2479 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1QUN2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: 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.: 1
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Protein (35.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Glucuronate); Reservoir (0.2 M Sodium chloride, 0.1 M Phosphate-citrate, pH 4.2, 20 %(w/v) PEG 8000); Cryoprotection (20% glycerol, 80% reservoir)

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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: Mar 1, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→80.33 Å / Num. obs: 40251 / % possible obs: 97.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.18 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.046 / Net I/σ(I): 12.3 / Num. measured all: 307566 / Scaling rejects: 34
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.4 / Num. measured all: 14421 / Num. unique all: 2408 / Rpim(I) all: 0.344 / Rejects: 0 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementResolution: 1.8→47.086 Å / FOM work R set: 0.916 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 2027 5.04 %
Rwork0.1425 38202 -
obs0.1437 40229 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.75 Å2 / Biso mean: 23.13 Å2 / Biso min: 5.68 Å2
Refinement stepCycle: final / Resolution: 1.8→47.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 15 319 2702
Biso mean--14.85 35.39 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012478
X-RAY DIFFRACTIONf_angle_d1.2243375
X-RAY DIFFRACTIONf_chiral_restr0.076357
X-RAY DIFFRACTIONf_plane_restr0.007457
X-RAY DIFFRACTIONf_dihedral_angle_d12.786924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.23221640.211227252889100
1.845-1.89490.23251340.186127512885100
1.8949-1.95070.20041460.173327512897100
1.9507-2.01360.19111520.154927532905100
2.0136-2.08560.18331580.134827562914100
2.0856-2.16910.16461340.126927622896100
2.1691-2.26780.15461480.123927632911100
2.2678-2.38740.16271340.11927862920100
2.3874-2.5370.16751340.12992801293599
2.537-2.73280.15481400.12682781292199
2.7328-3.00780.17921570.13982752290998
3.0078-3.44290.16131440.14652701284595
3.4429-4.33720.13591510.1332546269789
4.3372-47.1020.15761310.15272574270584
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)
11.7244-0.74710.69952.0819-0.75211.4470.00960.0213-0.0361-0.003-0.0418-0.21530.10720.17550.03910.16930.01620.020.189-0.00450.141962.8384-52.514915.4403
20.768-0.00860.0070.54660.0350.6106-0.01630.0417-0.0137-0.03920.02920.08470.073-0.0405-0.0120.1717-0.02060.00160.15590.00630.155246.4825-46.189616.0621
30.5907-0.70990.45034.0512-2.14051.63580.02250.00890.03050.0208-0.0503-0.110.0740.11880.02430.1716-0.0114-0.00970.14710.00460.127660.9254-43.628820.9622
41.18190.6585-0.76130.7291-0.4381.22430.1172-0.06520.24480.0489-0.10320.1754-0.2301-0.0564-0.0010.1704-0.01690.00220.1443-0.00480.208934.6924-35.335820.9148
54.39592.2014-0.17232.9176-0.80932.34090.098-0.26850.21810.24290.03270.1788-0.1032-0.066-0.12140.1684-0.0210.05030.2035-0.00440.200838.1653-43.89135.0551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 62 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 257 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 292 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 293 through 321 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 322 through 336 )A0

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