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- PDB-4p47: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4p47
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM OCHROBACTRUM ANTHROPI (Oant_4429), TARGET EFI-510151, C-TERMIUS BOUND IN LIGAND BINDING POCKET
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
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
TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 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 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Data collection
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references ...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 / software / struct_keywords
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
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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


Theoretical massNumber of molelcules
Total (without water)38,0511
Polymers38,0511
Non-polymers00
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.183, 68.695, 76.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 38050.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: ATCC 49188 / Gene: Oant_4429 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6X7C5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 1.87 Å3/Da / Density % sol: 34.19 % / Description: Thick Leaf Peddles
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (40.24 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.2 M Ammonium Sulfate, 20 %(w/v) PEG 3350); Cryoprotection (20% ethylene glycol, 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: Oct 17, 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: 1.3→25.535 Å / Num. all: 70496 / Num. obs: 70496 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 10.59 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.116 / Rsym value: 0.108 / Net I/av σ(I): 4.825 / Net I/σ(I): 9.9 / Num. measured all: 493001
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
1.3-1.376.20.782161852100370.3310.7822.498.6
1.37-1.456.90.5891.36663695920.2350.5893.499.5
1.45-1.5570.38526358090930.1540.385599.7
1.55-1.687.10.2622.96026985170.1040.2626.999.9
1.68-1.847.20.1824.25615678120.0720.1829.1100
1.84-2.067.30.1166.25195471170.0460.11612.8100
2.06-2.377.30.1085.94648563450.0430.10816.7100
2.37-2.917.30.0936.53935253720.0370.09319.6100
2.91-4.117.20.05510.83059142260.0220.05524.8100
4.11-25.5356.80.05410.81612623850.0230.0542597.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.3→23.935 Å / FOM work R set: 0.8972 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3562 5.06 %Random Selection
Rwork0.1635 66867 --
obs0.1648 70429 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.57 Å2 / Biso mean: 14.88 Å2 / Biso min: 4.95 Å2
Refinement stepCycle: final / Resolution: 1.3→23.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 491 2983
Biso mean---24.98 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092589
X-RAY DIFFRACTIONf_angle_d1.2533511
X-RAY DIFFRACTIONf_chiral_restr0.07397
X-RAY DIFFRACTIONf_plane_restr0.007465
X-RAY DIFFRACTIONf_dihedral_angle_d13.367982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31780.28311320.2742577270997
1.3178-1.33660.29471430.25472595273899
1.3366-1.35660.22021260.23842663278999
1.3566-1.37780.26011370.22212604274199
1.3778-1.40040.22651530.20182636278999
1.4004-1.42450.24411270.201926692796100
1.4245-1.45040.22411070.19752658276599
1.4504-1.47830.22781430.19182654279799
1.4783-1.50850.21891330.182826802813100
1.5085-1.54130.20031400.165126362776100
1.5413-1.57710.18841500.161126232773100
1.5771-1.61660.1811660.152126672833100
1.6166-1.66030.20051390.147626762815100
1.6603-1.70910.17481560.155726482804100
1.7091-1.76420.1761450.148926802825100
1.7642-1.82730.16741480.150326632811100
1.8273-1.90040.20011540.146926792833100
1.9004-1.98690.19021280.147526902818100
1.9869-2.09160.14991310.14527142845100
2.0916-2.22250.16051540.14126882842100
2.2225-2.3940.16191550.147426972852100
2.394-2.63460.19291450.156527382883100
2.6346-3.01520.18731700.16327162886100
3.0152-3.79640.17961390.153527712910100
3.7964-23.93890.17961410.16832845298698
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)
10.2224-0.2827-0.02460.2033-0.04810.2165-0.01710.0697-0.11960.04590.1251-0.18160.03490.18830.00210.0928-0.0026-0.01750.0996-0.02510.09613.0456-3.23435.7546
20.87520.29690.22360.57380.15390.11610.01330.00140.05390.08250.0006-0.00260.02180.0129-00.0618-00.00780.04630.00050.03870.55731.239130.816
30.47280.0226-0.14740.30140.07890.33610.0611-0.02120.05580.0095-0.07680.12190.0552-0.05780.01270.0731-0.0033-0.0020.0732-0.010.0688-22.2235-11.372926.2104
40.58640.26320.16530.55460.16730.11160.00390.0255-0.01520.02380.015-0.07870.01430.0167-0.07290.05780.0019-0.00130.0511-0.00250.0479-1.9019-5.533924.3196
50.58040.0288-0.04220.1547-0.01660.09390.02860.02760.1404-0.0533-0.07190.0792-0.0611-0.05650.00680.10350.0154-0.00420.1062-0.00880.0937-20.61011.801419.2203
6-0.0880.00130.0213-0.31850.0880.044-0.06140.02430.2008-0.0245-0.02720.10720.0332-0.1063-00.1718-0.01490.02510.1511-0.00550.1721-12.363611.801213.6911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 42 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 156 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 205 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 289 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 290 through 319 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 345 )A0

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