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- PDB-2zzw: Crystal Structure of a Periplasmic Substrate Binding Protein in C... -

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Basic information

Entry
Database: PDB / ID: 2zzw
TitleCrystal Structure of a Periplasmic Substrate Binding Protein in Complex with Zinc and Lactate
ComponentsABC transporter, solute-binding protein
KeywordsTRANSPORT PROTEIN / periplasmic substrate binding protein / zinc / lactate / TRAP transporter
Function / homology
Function and homology information


lactate transport / tripartite ATP-independent periplasmic transporter complex / transmembrane transport / periplasmic space / calcium ion binding / protein homodimerization activity / zinc ion binding
Similarity search - Function
Lactate-binding periplasmic protein TTHA0766 / 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 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LACTIC ACID / Lactate-binding periplasmic protein TTHA0766
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAkiyama, N. / Takeda, K. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of a periplasmic substrate-binding protein in complex with calcium lactate
Authors: Akiyama, N. / Takeda, K. / Miki, K.
History
DepositionFeb 27, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_validate_chiral.auth_atom_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, solute-binding protein
B: ABC transporter, solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9356
Polymers81,6242
Non-polymers3114
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-15 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.701, 84.986, 113.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter, solute-binding protein


Mass: 40811.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA0766 / Plasmid: PET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SK82
#2: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.27 Å3/Da / Density % sol: 45.73 % / Description: The file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.18M zinc acetate, 0.09M MES, pH6.5, 16% PEG 8000, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 92571 / % possible obs: 95.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 5.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 20
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6 / Num. unique all: 4864 / Rsym value: 0.178 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2744279.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED, the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4638 5 %RANDOM
Rwork0.151 ---
obs0.151 92571 88.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3676 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å20 Å2
2--3.41 Å20 Å2
3----0.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 14 662 5950
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 1.95→2.04 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.226 503 5.2 %
Rwork0.186 9216 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4lac_paramlac_top

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