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- PDB-4yic: CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (I... -

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Database: PDB / ID: 4yic
TitleCRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID
ComponentsTRAP TRANSPORTER SOLUTE BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


organic acid transport / tripartite ATP-independent periplasmic transporter complex / organic acid binding / transmembrane transport / rRNA processing / periplasmic space / ribosome / structural constituent of ribosome / translation / metal ion binding / cytoplasm
Similarity search - Function
Alpha-keto acid binding periplasmic protein / Solute binding protein, TakP-like / 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 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily ...Alpha-keto acid binding periplasmic protein / Solute binding protein, TakP-like / 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 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDINE-2-CARBOXYLIC ACID / ACETATE ION / IMIDAZOLE / Trap transporter solute binding protein / 40S ribosomal protein S21
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / 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: To be published
Title: CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP TRANSPORTER SOLUTE BINDING PROTEIN
B: TRAP TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,65510
Polymers85,0822
Non-polymers5738
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-53 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.681, 86.141, 72.339
Angle α, β, γ (deg.)90.000, 100.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TRAP TRANSPORTER SOLUTE BINDING PROTEIN


Mass: 42541.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: X5ID49, UniProt: A0A0J9X284*PLUS

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Non-polymers , 5 types, 743 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 1mM CaCl2, 1 mM Picolinic Acid); Reservoir ((MCSG2 B7 D3)(0.1 M Bis-Tris Propane pH 7.0, 2.8 M Sodium Acetate pH 7.0)); 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: Feb 11, 2015 / 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: 1.6→27.15 Å / Num. obs: 101931 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Net I/σ(I): 10.7 / Num. measured all: 379830 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.633.70.8351.61835049940.7150.50198.8
8.76-27.153.30.02129.517605340.9990.01481.5

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HZL

2hzl


Resolution: 1.6→25.562 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1729 5011 4.92 %
Rwork0.1427 96753 -
obs0.1442 101764 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.77 Å2 / Biso mean: 32.2181 Å2 / Biso min: 13.63 Å2
Refinement stepCycle: final / Resolution: 1.6→25.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 51 735 6146
Biso mean--38.41 40.82 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015550
X-RAY DIFFRACTIONf_angle_d1.2137521
X-RAY DIFFRACTIONf_chiral_restr0.05773
X-RAY DIFFRACTIONf_plane_restr0.007985
X-RAY DIFFRACTIONf_dihedral_angle_d13.3932003
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 (%)
1.6-1.61820.36781710.31453186335798
1.6182-1.63720.3041680.28263186335499
1.6372-1.65720.29651660.27283218338498
1.6572-1.67820.30951730.25673150332399
1.6782-1.70020.28761800.25043187336799
1.7002-1.72350.23041580.23393196335499
1.7235-1.74810.28241690.23333199336899
1.7481-1.77420.22711530.20363196334999
1.7742-1.80190.22271720.19633204337699
1.8019-1.83150.23481810.1973189337099
1.8315-1.8630.23191790.18813203338299
1.863-1.89690.20931480.17783241338999
1.8969-1.93340.20751380.16243211334999
1.9334-1.97280.20881650.15673212337799
1.9728-2.01570.20521710.1513232340399
2.0157-2.06260.16511690.14383228339799
2.0626-2.11410.1651500.1393239338999
2.1141-2.17130.16621460.138732453391100
2.1713-2.23510.16811580.136232873445100
2.2351-2.30720.16591850.129532173402100
2.3072-2.38960.14941700.125432533423100
2.3896-2.48520.16581710.124332333404100
2.4852-2.59820.16771930.128732253418100
2.5982-2.73510.14881640.128932543418100
2.7351-2.90620.16041830.134732543437100
2.9062-3.13020.15381740.13732583432100
3.1302-3.44460.16181620.131932613423100
3.4446-3.94150.15691630.117132713434100
3.9415-4.95990.12041760.103132783454100
4.9599-25.56570.16091550.13193240339596
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)
10.35940.1703-0.21270.3664-0.19750.186-0.27330.1294-0.1086-0.49890.12650.06980.607-0.2193-0.05040.3283-0.1817-0.09010.313-0.04110.261-0.454831.2171-24.2924
20.4490.3183-0.30210.6638-0.35460.3421-0.04240.14690.0896-0.24960.08590.113-0.0465-0.14540.00010.2457-0.0187-0.06420.24360.01270.20386.344747.5325-24.8856
30.1515-0.1326-0.02730.34310.05150.1238-0.11560.1314-0.0295-0.33080.0257-0.08970.10660.0411-0.01730.3142-0.01720.07550.24790.01040.191630.802343.7601-29.2784
40.0948-0.10110.0290.0597-0.06420.19270.00520.1354-0.0326-0.2194-0.03-0.0140.08410.081300.357-0.02530.03520.2150.00040.161224.05240.2858-32.5418
50.29770.0175-0.08370.2895-0.39480.542-0.00080.02540.0286-0.33830.01860.03860.1229-0.0270.02050.2584-0.0232-0.03330.2075-0.00480.197614.073441.2634-25.1547
60.08440.1086-0.1710.2052-0.2650.4528-0.05210.0055-0.1218-0.20990.02570.05290.2335-0.0572-0.0120.2237-0.0357-0.01070.2057-0.0140.2111.456333.4448-16.2376
70.3040.1547-0.28180.1023-0.18170.51830.00320.07670.1379-0.2889-0.0471-0.1256-0.14740.2032-0.00160.2873-0.03450.00260.23730.03940.242127.624153.6803-23.4798
80.16420.0966-0.09220.12760.04550.11850.0147-0.04350.1402-0.0453-0.04230.0367-0.21030.04210.00120.23190.0069-0.00960.16430.01980.230815.153958.0322-12.5381
90.18790.2219-0.10770.2024-0.10340.2537-0.0288-0.0883-0.0444-0.1562-0.048-0.219-0.0020.1731-0.00230.15490.0160.03610.24410.04210.25232.475134.7869-1.009
100.30670.04610.11160.5989-0.08620.278-0.042-0.03020.03350.18180.07290.2762-0.0842-0.2420.05960.1124-0.0410.02370.27960.00840.3102-5.869537.11163.9831
110.4442-0.00220.14740.2539-0.18670.3154-0.0408-0.0339-0.0938-0.0534-0.00070.06910.2449-0.0329-00.228-0.03740.02570.18130.00320.21749.136228.41523.0508
120.1144-0.18390.04570.439-0.1630.3226-0.1068-0.11610.01470.170.02880.06420.04010.0245-0.01150.19470.0071-0.00680.2126-0.00220.151620.363342.980217.0988
13-0.0045-0.0318-0.00480.1773-0.02630.0550.0434-0.07130.01660.1231-0.00880.0948-0.1080.0142-00.20450.00230.02050.1974-0.00070.1929.84549.613415.9808
140.3277-0.1531-0.12360.1184-0.17810.4893-0.03550.0072-0.03180.08570.03660.02460.0853-0.03610.00010.1568-0.0270.0060.172-0.0080.20548.96738.76396.9388
150.1622-0.1208-0.05470.0707-0.06330.3102-0.06040.0044-0.0032-0.08560.05270.084-0.05-0.14660.00010.1459-0.0302-0.01760.2062-0.00020.21635.204844.2526-3.1403
160.40030.13680.26390.1001-0.07980.4719-0.0114-0.1017-0.03330.1877-0.0492-0.11660.07360.2272-00.20870.0331-0.00620.2530.03240.228127.077937.361311.2314
170.47110.0096-0.05320.0260.09620.7616-0.0467-0.02390.0031-0.129-0.0495-0.09390.09280.1885-0.00010.1646-0.00030.00490.19290.00760.191625.560741.7858-6.0496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 73 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 154 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 182 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 226 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 260 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 295 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 296 through 326 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 327 through 349 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 350 through 373 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 89 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 154 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 155 through 199 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 226 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 227 through 260 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 261 through 295 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 296 through 325 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 326 through 374 )B0

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