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- PDB-5cm6: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 5cm6
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOALTEROMONAS ATLANTICA T6c(Patl_2292, TARGET EFI-510180) WITH BOUND SODIUM AND PYRUVATE
ComponentsTRAP dicarboxylate transporter-DctP subunit
KeywordsTRANSPORT PROTEIN / Solute binding protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


tripartite ATP-independent periplasmic transporter complex / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / TRAP dicarboxylate transporter-DctP subunit
Similarity search - Component
Biological speciesPseudoalteromonas atlantica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, 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)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOALTEROMONAS ATLANTICA T6c(Patl_2292, TARGET EFI-510180) WITH BOUND SODIUM AND PYRUVATE
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, 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.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionJul 29, 2015ID: 4X26
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

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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
B: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2616
Polymers83,0382
Non-polymers2224
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-58 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.345, 83.345, 198.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TRAP dicarboxylate transporter-DctP subunit


Mass: 41519.242 Da / Num. of mol.: 2 / Fragment: solute binding protein (UNP residues 23-357)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas atlantica (bacteria) / Strain: T6c / ATCC BAA-1087 / Gene: Patl_2292 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15TH9
#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (40.2 mg/ml, 20 mM TRIS pH 8.0, 5 mM DTT, 150 mM NaCl, 5% Glycerol, 10 mM Pyruvate, 1 mM CaCl2); Reservoir (0.2 M Ammonium fluoride, 20 %(w/v) PEG 3350); Cryoprotection (80% ...Details: Protein (40.2 mg/ml, 20 mM TRIS pH 8.0, 5 mM DTT, 150 mM NaCl, 5% Glycerol, 10 mM Pyruvate, 1 mM CaCl2); Reservoir (0.2 M Ammonium fluoride, 20 %(w/v) PEG 3350); 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: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 26, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 62371 / % possible obs: 99.8 % / Redundancy: 14.4 % / Biso Wilson estimate: 20.82 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Χ2: 0.938 / Net I/av σ(I): 24.684 / Net I/σ(I): 6.1 / Num. measured all: 898089
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRmerge(I) obsRpim(I) allRrim(I) all
1.83-1.8612.330100.4150.77497.9
1.86-1.914.330730.6030.82399.9
1.9-1.9314.530510.7621.1741000.9580.2570.992
1.93-1.9714.530710.7870.8431000.59
1.97-2.0114.630510.8630.8441000.318
2.01-2.0614.630890.9160.8541000.810.2170.839
2.06-2.1114.630790.9280.8721000.6720.1790.695
2.11-2.1714.730880.9560.8911000.5730.1530.594
2.17-2.2314.730980.9670.9261000.6020.1610.623
2.23-2.3114.630970.9641.4661000.4130.1110.428
2.31-2.3914.731010.9880.8581000.2840.0760.294
2.39-2.4814.830860.990.8481000.2270.0610.235
2.48-2.614.731200.9940.8281000.1720.0460.178
2.6-2.7314.730970.9950.7941000.1390.0370.144
2.73-2.914.731390.9970.7561000.110.0290.113
2.9-3.1314.631540.9970.8431000.0980.0260.102
3.13-3.4414.631510.9951.341000.1060.0290.11
3.44-3.9314.132010.9951.7741000.1080.0290.112
3.93-4.9414.332350.9980.8461000.0630.0170.066
4.94-2013.433800.9990.3998.50.040.0110.041

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIXphasing
RefinementResolution: 1.83→19.966 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 2919 4.92 %
Rwork0.1842 56402 -
obs0.1872 59321 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.65 Å2 / Biso mean: 30.5671 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: final / Resolution: 1.83→19.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 20 535 5845
Biso mean--21.56 32.73 -
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125454
X-RAY DIFFRACTIONf_angle_d1.3297370
X-RAY DIFFRACTIONf_chiral_restr0.053757
X-RAY DIFFRACTIONf_plane_restr0.007948
X-RAY DIFFRACTIONf_dihedral_angle_d14.8512004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.86190.3767750.30811281135646
1.8619-1.8940.57441050.44591939204470
1.894-1.92840.47181420.38952477261990
1.9284-1.96540.36151420.29632715285798
1.9654-2.00550.3161360.240927702906100
2.0055-2.04910.28271350.208727722907100
2.0491-2.09670.2621500.198627852935100
2.0967-2.14910.27271570.195427502907100
2.1491-2.20710.24491260.214727972923100
2.2071-2.2720.30851580.2527902948100
2.272-2.34520.2741390.21032768290799
2.3452-2.42890.24121320.173928132945100
2.4289-2.52590.23981570.160127912948100
2.5259-2.64060.20851240.160528292953100
2.6406-2.77950.2171690.151328112980100
2.7795-2.95320.23441520.171628092961100
2.9532-3.18030.251410.179428262967100
3.1803-3.49880.2151570.164228553012100
3.4988-4.00160.20751240.15142871299599
4.0016-5.02820.16681640.131528913055100
5.0282-19.96670.22081340.17383062319699
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)
10.02490.00460.02170.04620.0570.08810.05630.08370.1213-0.07530.0985-0.0329-0.1242-0.02480.05350.22170.01640.07410.07460.06630.2147-3.885267.618316.0631
20.0109-0.00170.00430.01110.0040.0041-0.00010.16550.0426-0.01210.0430.0353-0.0452-0.16080.01560.06930.0545-0.06240.23830.06330.0109-15.773852.831419.5748
30.00180.0010.00060.00160.00180.0013-0.0118-0.02670.01370.04330.04590.03910.0166-0.0142-0.00030.17840.07280.00430.14570.02040.1168-18.797755.734844.9093
40.0774-0.0257-0.02450.05050.02640.0145-0.01070.090.1506-0.02050.0149-0.0439-0.0666-0.03710.03050.08210.1014-0.03120.13260.02990.123-12.189459.758432.5446
50.00610.0072-0.00460.03160.00210.01390.01690.00190.048-0.0370.1157-0.0904-0.00140.01410.03010.05620.0056-0.03250.1309-0.02880.0890.108853.527321.3035
60.0135-0.0143-0.01840.00810.01470.02020.03380.0176-0.00640.1370.06950.00140.0153-0.0124-00.14220.0386-0.04470.19740.02990.1207-18.97547.82738.2986
70.0281-0.0082-0.00070.02540.01860.0198-0.06940.0387-0.04340.0480.003-0.02720.0783-0.0861-0.00440.09720.0088-0.01860.17610.00650.1072-12.931636.04525.1358
80.0062-0.0061-0.00030.0304-0.01030.00490.00970.00920.0044-0.01460.0294-0.0024-0.0208-0.00520.05220.1159-0.17530.03430.2357-0.08610.12285.034743.14430.6899
90.1291-0.01610.00250.22850.09120.1338-0.0890.0905-0.099-0.04050.2281-0.16710.10340.13990.09810.0874-0.0409-0.0040.1496-0.12640.203311.651634.41213.9286
100.0027-0.0035-0.00090.00380.00030.001-0.020.0232-0.013-0.0060.0175-0.02940.02120.0043-00.220.0945-0.05830.2373-0.09010.320210.802119.50115.4351
110.001-0.00590.01390.0030.00570.0174-0.03030.0414-0.0583-0.0230.1319-0.14110.08860.09070.0628-0.0428-0.1896-0.0879-0.0206-0.11710.07922.375733.208212.1252
120.0039-0.0033-0.00190.0106-0.00380.0041-0.00580.00710.0054-0.00180.0645-0.03480.1303-0.00450.00010.23960.0459-0.08640.1558-0.00630.27697.584322.651628.7252
130.0219-0.03040.06050.1334-0.11630.17320.0228-0.0171-0.05370.03960.0764-0.04810.02820.01950.13650.04490.1272-0.12860.1016-0.03860.09154.628540.1832.7397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:92 )A26 - 92
2X-RAY DIFFRACTION2( CHAIN A AND RESID 93:154 )A93 - 154
3X-RAY DIFFRACTION3( CHAIN A AND RESID 155:175 )A155 - 175
4X-RAY DIFFRACTION4( CHAIN A AND RESID 176:253 )A176 - 253
5X-RAY DIFFRACTION5( CHAIN A AND RESID 254:287 )A254 - 287
6X-RAY DIFFRACTION6( CHAIN A AND RESID 288:321 )A288 - 321
7X-RAY DIFFRACTION7( CHAIN A AND RESID 322:356 )A322 - 356
8X-RAY DIFFRACTION8( CHAIN B AND ( RESID 26:56 OR RESID 57:57 ) )B26 - 56
9X-RAY DIFFRACTION8( CHAIN B AND ( RESID 26:56 OR RESID 57:57 ) )B57
10X-RAY DIFFRACTION9( CHAIN B AND RESID 58:175 )B58 - 175
11X-RAY DIFFRACTION10( CHAIN B AND RESID 176:202 )B176 - 202
12X-RAY DIFFRACTION11( CHAIN B AND RESID 203:289 )B203 - 289
13X-RAY DIFFRACTION12( CHAIN B AND RESID 290:321 )B290 - 321
14X-RAY DIFFRACTION13( CHAIN B AND RESID 322:354 )B322 - 354

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