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- PDB-4yzz: Crystal structure of a TRAP transporter solute binding protein (I... -

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Basic information

Entry
Database: PDB / ID: 4yzz
TitleCrystal structure of a TRAP transporter solute binding protein (IPR025997) from Bordetella bronchiseptica RB50 (BB0280, TARGET EFI-500035) mixed occupancy dimer, copurified calcium and picolinate bound active site versus apo site
ComponentsTRAP TRANSPORTER SOLUTE BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / TRAP TRANSPORTER SOLUTE BINDING 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 / periplasmic space / metal ion binding
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...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 / 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 / DI(HYDROXYETHYL)ETHER / Putative exported protein
Similarity search - Component
Biological speciesBORDETELLA BRONCHISEPTICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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) mixed occupancy dimer, copurified calcium and ...Title: Crystal structure of a TRAP transporter solute binding protein (IPR025997) from Bordetella bronchiseptica RB50 (BB0280, TARGET EFI-500035) mixed occupancy dimer, copurified calcium and picolinate bound active site versus apo site
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 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
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 / struct_keywords
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 / _struct_keywords.text
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.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
D: TRAP TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0567
Polymers80,4732
Non-polymers5835
Water16,574920
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-36 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.249, 50.104, 96.556
Angle α, β, γ (deg.)90.000, 104.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein TRAP TRANSPORTER SOLUTE BINDING PROTEIN


Mass: 40236.676 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: A0A0H3LP08*PLUS

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Non-polymers , 5 types, 925 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 920 / 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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 1mM CaCl2, 1 mM Picolinic Acid); Reservoir (MCSG2 (E8) 0.1 M CHES pH 9.5, 20 %(w/v) PEG 8000); Cryoprotection (20% diethylene 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: 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: 1.3→25.42 Å / Num. obs: 138836 / % possible obs: 95.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 9.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.045 / Net I/σ(I): 11.5 / Num. measured all: 526365 / Scaling rejects: 82
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
1.3-1.323.30.5832.11926758080.7970.35880.6
7.12-25.423.40.0293127908180.9980.01887.1

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YIC

4yic


Resolution: 1.3→24.198 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.163 6812 4.91 %
Rwork0.1388 131982 -
obs0.14 138794 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.62 Å2 / Biso mean: 14.725 Å2 / Biso min: 6.4 Å2
Refinement stepCycle: final / Resolution: 1.3→24.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 37 920 6197
Biso mean--15.57 25.42 -
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085484
X-RAY DIFFRACTIONf_angle_d1.2737444
X-RAY DIFFRACTIONf_chiral_restr0.071767
X-RAY DIFFRACTIONf_plane_restr0.007973
X-RAY DIFFRACTIONf_dihedral_angle_d13.2291994
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 (%)
1.3-1.31480.27331900.25933606379678
1.3148-1.33020.28212010.25664057425889
1.3302-1.34650.2822340.23884299453393
1.3465-1.36350.25051930.23114346453994
1.3635-1.38140.22792350.22424349458494
1.3814-1.40040.23062120.21674339455194
1.4004-1.42040.22092280.20564324455294
1.4204-1.44160.22122150.1974342455794
1.4416-1.46410.18372130.19374404461795
1.4641-1.48810.19482120.17874379459195
1.4881-1.51370.20162250.16664372459795
1.5137-1.54130.19422390.15594354459395
1.5413-1.57090.15812310.1444434466595
1.5709-1.6030.16592160.14434390460695
1.603-1.63780.19192200.13864402462295
1.6378-1.67590.16712450.13574429467496
1.6759-1.71780.17632160.13624439465596
1.7178-1.76420.16492210.13584422464396
1.7642-1.81610.15922250.13254495472096
1.8161-1.87470.14852410.12684411465296
1.8747-1.94170.16172690.12254473474297
1.9417-2.01940.12942400.11834473471397
2.0194-2.11130.14262550.11524447470297
2.1113-2.22250.12992300.11194538476897
2.2225-2.36170.13252520.11084513476597
2.3617-2.54380.13972480.11774541478998
2.5438-2.79950.14772500.12264546479698
2.7995-3.20380.16541990.13024630482998
3.2038-4.03340.14762200.12194649486998
4.0334-24.20240.14992370.13074579481695
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)
10.4192-0.0925-0.10020.38140.15280.12820.0007-0.11260.10980.02040.0169-0.0239-0.08280.01160.00010.1029-0.0007-0.0030.1154-0.01230.102523.594510.291136.127
20.26060.08050.1240.129-0.09810.24170.0085-0.10750.1360.00030.0084-0.0441-0.06810.077300.1185-0.0093-0.00110.136-0.01650.121731.95267.722735.6582
30.333-0.1060.12060.30420.10380.4954-0.002-0.0464-0.03810.01660.0205-0.01670.01720.046800.08220.0050.00130.08660.00670.086125.0786-6.702328.9144
40.7659-0.1013-0.00650.5193-0.10410.4733-0.00550.03190.02690.01240.0001-0.0395-0.03550.0642-00.1043-0.0105-0.00320.10060.0020.090130.55363.62029.1879
50.478-0.04410.07330.1890.15720.1674-0.0282-0.00140.0293-0.01490.01650.0014-0.01590.012800.0825-0.00030.00040.06940.0020.086725.58642.039922.1852
60.4141-0.0283-0.14810.1580.2040.29280.0071-0.01850.0518-0.01620.02060.0088-0.0624-0.039500.08390.00360.00210.0835-0.00160.087815.4157.814525.8219
70.44740.1697-0.14410.33540.20190.42050.05390.0853-0.0929-0.1175-0.0440.08570.08010.045-00.10460.0021-0.0060.1024-0.01570.097425.0918-9.62697.7992
80.1563-0.0005-0.14410.28590.0360.13660.0180.0519-0.2098-0.0202-0.04240.06540.0842-0.0141-0.00010.10980.00670.00840.09010.00240.129616.276-16.693720.2817
90.6015-0.13050.25360.09740.04980.3127-0.0550.19810.1885-0.0101-0.0527-0.1184-0.12620.0654-0.0190.1011-0.0044-0.00630.13020.01680.11150.37450.68039.1051
100.6390.0625-0.10630.49370.14830.44460.0111-0.1019-0.04330.0388-0.00610.02360.0457-0.062200.0992-0.00710.00350.1023-0.0050.0896-4.260.265942.7319
110.39130.0166-0.01070.02820.01180.51250.00520.00570.02010.0004-0.00290.0137-0.0146-0.033300.08520.0003-0.00360.0841-0.00080.0937-3.95553.92524.5948
120.4939-0.18520.06150.2994-0.1250.21370.0067-0.124-0.05840.07430.01160.0379-0.0242-0.034400.0977-0.0167-0.00410.1235-0.00530.1003-16.1552-12.270521.1994
130.36360.09050.11030.11920.11520.4359-0.0019-0.0037-0.0392-0.00150.02260.00930.0228-0.003400.0841-0.0065-0.00180.0874-0.00570.09360.4911-3.26530.7124
140.44420.230.27040.19810.04930.5695-0.00060.06880.0063-0.0686-0.02290.05370.0073-0.0092-0.00050.0848-0.0116-0.00210.09760.00580.0966-11.2967-0.353811.4037
150.66270.043-0.2790.04130.11380.52620.03190.13620.0297-0.0445-0.0284-0.00040.0192-0.035700.0916-0.0048-0.00360.0971-0.00040.11794.61453.135913.3144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 64 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 89 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 154 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 155 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 366 )A0
10X-RAY DIFFRACTION10chain 'D' and (resid 31 through 107 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 108 through 169 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 170 through 230 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 231 through 295 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 296 through 325 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 326 through 366 )D0

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