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- PDB-2hzl: Crystal structures of a sodium-alpha-keto acid binding subunit fr... -

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Basic information

Entry
Database: PDB / ID: 2hzl
TitleCrystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in its closed forms
ComponentsTRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
KeywordsLIGAND BINDING / TRANSPORT PROTEIN / TRAP transporter / periplasmic subunit
Function / homology
Function and homology information


tripartite ATP-independent periplasmic transporter complex / carboxylic acid transport / organic acid binding / transmembrane transport / periplasmic space / protein homodimerization activity / 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
PYRUVIC ACID / Alpha-keto acid-binding periplasmic protein TakP
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGonin, S. / Arnoux, P. / Pierru, B. / Alonso, B. / Sabaty, M. / Pignol, D.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding.
Authors: Gonin, S. / Arnoux, P. / Pierru, B. / Lavergne, J. / Alonso, B. / Sabaty, M. / Pignol, D.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / struct_site
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.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.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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
B: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3487
Polymers80,0382
Non-polymers3105
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-62 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.021, 78.057, 95.139
Angle α, β, γ (deg.)90.00, 124.98, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer

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Components

#1: Protein TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM


Mass: 40019.129 Da / Num. of mol.: 2 / Fragment: SkaP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Species: Rhodobacter sphaeroides / Strain: ATCC 17023 / Plasmid: pET101 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3J1R2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 100mM sodium citrate 1.4M ammonium sulfate 30mM pyruvate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 1.4→48 Å / Num. all: 137400 / Num. obs: 137318 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.4→1.41 Å / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HZK

2hzk


Resolution: 1.4→39.01 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.784 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 6908 5 %RANDOM
Rwork0.173 ---
all0.173 137400 --
obs0.173 137316 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.06 Å2
2--0.01 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 20 471 5795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225488
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.9327482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89624.308253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76915825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7481518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024332
X-RAY DIFFRACTIONr_nbd_refined0.2060.22905
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2398
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.214
X-RAY DIFFRACTIONr_mcbond_it0.5371.53364
X-RAY DIFFRACTIONr_mcangle_it1.03825386
X-RAY DIFFRACTIONr_scbond_it1.70132257
X-RAY DIFFRACTIONr_scangle_it2.7614.52090
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 510 -
Rwork0.243 9499 -
obs-10009 100 %

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