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- PDB-2hpg: The crystal structure of a thermophilic TRAP periplasmic binding ... -

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Basic information

Entry
Database: PDB / ID: 2hpg
TitleThe crystal structure of a thermophilic TRAP periplasmic binding protein
ComponentsABC transporter, periplasmic substrate-binding proteinATP-binding cassette transporter
KeywordsLIGAND BINDING PROTEIN / periplasmic binding protein / thermophilic proteins / TRAP-transport
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / 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 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter, periplasmic substrate-binding protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCuneo, M.J. / Hellinga, H.W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport.
Authors: Cuneo, M.J. / Changela, A. / Miklos, A.E. / Beese, L.S. / Krueger, J.K. / Hellinga, H.W.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter, periplasmic substrate-binding protein
B: ABC transporter, periplasmic substrate-binding protein
C: ABC transporter, periplasmic substrate-binding protein
D: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)151,3514
Polymers151,3514
Non-polymers00
Water9,530529
1
A: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ABC transporter, periplasmic substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.260, 119.260, 429.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a monomer.

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Components

#1: Protein
ABC transporter, periplasmic substrate-binding protein / ATP-binding cassette transporter / TRAP-Periplasmic Binding Protein


Mass: 37837.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0322 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta / References: UniProt: Q9WYF8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M Phosphate/Citrate pH4.2, 2.5M Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97167, 0.97934, 0.97920
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971671
20.979341
30.97921
ReflectionResolution: 1.9→103.282 Å / Num. all: 142555 / Num. obs: 142555 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-28.40.4051.9171983204710.405100
2-2.128.90.3352.2173500194110.335100
2.12-2.279.40.2612.9172072182540.261100
2.27-2.459.80.2093.6167230170670.209100
2.45-2.6910.10.1584.7158510157680.158100
2.69-310.30.1126.5147350143540.112100
3-3.4710.20.0877.6129776127200.087100
3.47-4.2510.20.0659.8110703109020.065100
4.25-6.0110.10.05112.18706585940.051100
6.01-30.019.50.03913.94765350140.03999.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.906 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 7152 5 %RANDOM
Rwork0.213 ---
all0.215 142411 --
obs0.215 142411 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.493 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10353 0 0 529 10882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210615
X-RAY DIFFRACTIONr_bond_other_d0.0010.027372
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.96314375
X-RAY DIFFRACTIONr_angle_other_deg0.872318086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84451335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39825.071493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.701151985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5951545
X-RAY DIFFRACTIONr_chiral_restr0.0730.21540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022092
X-RAY DIFFRACTIONr_nbd_refined0.210.22276
X-RAY DIFFRACTIONr_nbd_other0.1830.27653
X-RAY DIFFRACTIONr_nbtor_refined0.180.25128
X-RAY DIFFRACTIONr_nbtor_other0.0850.25333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2511
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.217
X-RAY DIFFRACTIONr_mcbond_it0.8751.58058
X-RAY DIFFRACTIONr_mcbond_other0.131.52614
X-RAY DIFFRACTIONr_mcangle_it1.017210365
X-RAY DIFFRACTIONr_scbond_it1.75134895
X-RAY DIFFRACTIONr_scangle_it2.5614.53980
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 486 -
Rwork0.314 9847 -
obs-10333 100 %

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