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- PDB-2qry: Periplasmic thiamin binding protein -

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Basic information

Entry
Database: PDB / ID: 2qry
TitlePeriplasmic thiamin binding protein
ComponentsThiamine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / thiamin binding protein / periplasmic / ABC transporter
Function / homology
Function and homology information


thiamine binding / thiamine transmembrane transport / thiamine transport / thiamine pyrophosphate binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Thiamine/thiamin pyrophosphate-binding periplasmic protein, ABC transporter / Thiamin/thiamin pyrophosphate ABC transporter, substrate-binding protein, Proteobacteria / Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMIN PHOSPHATE / Thiamine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsEalick, S.E. / Soriano, E.V.
CitationJournal: Biochemistry / Year: 2008
Title: Structural Similarities between Thiamin-Binding Protein and Thiaminase-I Suggest a Common Ancestor
Authors: Soriano, E.V. / Rajashankar, K.R. / Hanes, J.W. / Bale, S. / Begley, T.P. / Ealick, S.E.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Thiamine-binding periplasmic protein
B: Thiamine-binding periplasmic protein
C: Thiamine-binding periplasmic protein
D: Thiamine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,6808
Polymers147,2984
Non-polymers1,3814
Water9,008500
1
A: Thiamine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1702
Polymers36,8251
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiamine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1702
Polymers36,8251
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiamine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1702
Polymers36,8251
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thiamine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1702
Polymers36,8251
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.040, 118.070, 90.330
Angle α, β, γ (deg.)90.00, 93.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiamine-binding periplasmic protein


Mass: 36824.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thiB, tbpA / Production host: Escherichia coli (E. coli) / References: UniProt: P31550
#2: Chemical
ChemComp-TPS / THIAMIN PHOSPHATE


Mass: 345.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18N4O4PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2.0 M (NH4)2SO4, 0.1 M Na citrate, and 0.2 M Na/K tartrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→49.39 Å / Num. all: 124110 / Num. obs: 61739 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 11.8
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.386 / % possible all: 81.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→49.39 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2574069.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3076 5 %RANDOM
Rwork0.198 ---
all0.2 124110 --
obs0.2 61739 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.4622 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å21.15 Å2
2---0.43 Å20 Å2
3---0.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.25→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9691 0 88 500 10279
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d2.2
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 491 5.1 %
Rwork0.255 9199 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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