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- PDB-4pe3: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4pe3
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (Rsph17029_3620, TARGET EFI-510199), APO OPEN STRUCTURE
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 / periplasmic space / metal ion binding
Similarity search - Function
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
ACETATE ION / IMIDAZOLE / TRAP dicarboxylate transporter-DctP subunit
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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)
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
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,15315
Polymers38,2391
Non-polymers91314
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.072, 97.938, 35.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TRAP dicarboxylate transporter-DctP subunit


Mass: 38239.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17029 / ATH 2.4.9 / Gene: Rsph17029_3620 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3PQU4

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Non-polymers , 5 types, 415 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.81 Å3/Da / Density % sol: 32.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (34.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Glycerate); Reservoir (0.2 M Zinc Acetate, 0.1 M Imidazole pH 6.5, 10%(w/v) PEG 8000); Cryoprotection (80% Reservoir, 20% Ethylene glycol)

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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: Apr 9, 2014 / 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: 1.35→26.36 Å / Num. obs: 61112 / % possible obs: 98.8 % / Redundancy: 14.4 % / Biso Wilson estimate: 12.24 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Net I/σ(I): 14.1 / Num. measured all: 878379 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.35-1.3714.20.9173.24198629600.24797.5
7.39-26.3611.10.0922744784050.02890.6

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.35→25.609 Å / FOM work R set: 0.8542 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 5926 5.09 %Random Selection
Rwork0.1692 110497 --
obs0.1706 116423 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.95 Å2 / Biso mean: 19.48 Å2 / Biso min: 6.18 Å2
Refinement stepCycle: final / Resolution: 1.35→25.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 47 401 2872
Biso mean--17.32 28.65 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182590
X-RAY DIFFRACTIONf_angle_d1.3023527
X-RAY DIFFRACTIONf_chiral_restr0.073383
X-RAY DIFFRACTIONf_plane_restr0.007467
X-RAY DIFFRACTIONf_dihedral_angle_d14.596933
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 (%)
1.35-1.36530.31962000.28883636383697
1.3653-1.38140.31772150.26613616383197
1.3814-1.39820.27952310.25833568379998
1.3982-1.41590.29852040.25123629383398
1.4159-1.43460.23522090.23793728393798
1.4346-1.45420.26652060.22223545375198
1.4542-1.4750.26151880.2163668385698
1.475-1.4970.23361740.21593716389098
1.497-1.52040.24432140.20043632384698
1.5204-1.54530.20971840.19253709389398
1.5453-1.5720.21332020.19223625382798
1.572-1.60060.22951480.1893700384898
1.6006-1.63130.1991810.18743747392899
1.6313-1.66460.19531800.17273660384099
1.6646-1.70080.18852220.17313728395099
1.7008-1.74040.18291920.16783646383899
1.7404-1.78390.22382080.16813683389199
1.7839-1.83210.19462240.16233658388299
1.8321-1.8860.17052090.16843724393399
1.886-1.94680.19522020.16163653385599
1.9468-2.01640.17672320.16213750398299
2.0164-2.09710.17841870.15583713390099
2.0971-2.19250.21551840.150136973881100
2.1925-2.3080.16621800.151137383918100
2.308-2.45250.1922160.15236853901100
2.4525-2.64170.1751680.154337733941100
2.6417-2.90720.17991800.16337633943100
2.9072-3.32710.2011970.158837453942100
3.3271-4.18880.17281980.146837093907100
4.1888-25.61390.18011910.16843653384497
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)
12.0259-0.33190.19894.05180.56913.09450.0013-0.05910.4350.2280.07680.1671-0.079-0.0899-0.06920.0725-0.00010.0110.11530.00040.18490.2766112.824346.5391
22.8492-0.1144-0.05621.2302-0.68740.61930.07570.61420.7294-0.1089-0.0432-0.0429-0.1522-0.3416-0.03560.13140.03020.01110.20720.10320.32611.9791117.108537.3575
31.05170.0219-0.23982.1586-0.00050.1466-0.01190.08440.28240.02050.0503-0.1962-0.02960.0223-0.02870.0714-0.0032-0.02710.09560.02130.150420.8221107.536639.2783
40.790.0578-0.27111.68260.02050.5665-0.04710.1216-0.0041-0.13380.0236-0.05830.0515-0.13870.01640.0956-0.0055-0.00590.121-0.00340.050417.708791.115534.8785
51.9222-0.0874-0.35311.98190.1410.6022-0.0542-0.04640.44710.29880.1066-0.30810.0048-0.0003-0.04980.09070.0055-0.060.0788-0.00740.137617.2193106.792845.8325
61.8586-0.79770.91862.1077-1.15843.0094-0.1116-0.07310.38890.0396-0.0617-1.1191-0.28070.1890.19150.06-0.0386-0.06630.14360.01450.539431.4376113.758439.7503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 77 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 117 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 193 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 260 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 340 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 341 through 363 )A0

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