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- PDB-5i5p: Crystal structure of a marine metagenome TRAP solute binding prot... -

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Basic information

Entry
Database: PDB / ID: 5i5p
TitleCrystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157) in complex with co-purified 4-hydroxybenzoate
ComponentsTRAP TRANSPORTER SOLUTE BINDING PROTEIN
KeywordsTRANSPORT PROTEIN
Function / homologyBacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / BROMIDE ION / DI(HYDROXYETHYL)ETHER / P-HYDROXYBENZOIC ACID
Function and homology information
Biological speciesuncultured marine bacterium (environmental samples)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Hogle, S.L. / Dupont, C.L. / Almo, S.C.
CitationJournal: To Be Published
Title: Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_ ...Title: Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157) in complex with co-purified 4-hydroxybenzoate
Authors: Vetting, M.W. / Al Obaidi, N.F. / Hogle, S.L. / Dupont, C.L. / Almo, S.C.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP TRANSPORTER SOLUTE BINDING PROTEIN
B: TRAP TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49514
Polymers75,3142
Non-polymers1,18012
Water13,493749
1
A: TRAP TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1416
Polymers37,6571
Non-polymers4845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3538
Polymers37,6571
Non-polymers6967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.305, 82.492, 76.577
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRAP TRANSPORTER SOLUTE BINDING PROTEIN


Mass: 37657.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured marine bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express
#2: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.15 M potassium Bromide, 30 %(w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.547 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 1, 2016 / Details: VariMax HF Arc Sec optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.547 Å / Relative weight: 1
ReflectionResolution: 1.599→100 Å / Num. obs: 70021 / % possible obs: 93.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.37 Å2 / Rmerge(I) obs: 0.084 / Net I/av σ(I): 25.19 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.633.80.333183.4
1.63-1.664.10.286185.2
1.66-1.694.10.271186.1
1.69-1.724.30.232186.9
1.72-1.764.40.2187.7
1.76-1.84.60.18187.7
1.8-1.854.70.166189
1.85-1.94.80.145189
1.9-1.9550.123190.5
1.95-2.025.10.109192.2
2.02-2.095.40.096193.4
2.09-2.175.70.091195.4
2.17-2.276.40.099198.2
2.27-2.397.70.102199.9
2.39-2.549.40.097199.9
2.54-2.7410.60.092199.9
2.74-3.0112.10.0841100
3.01-3.4514.20.0851100
3.45-4.3414.40.0741100
4.34-10012.70.075199.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5I7I

5i7i


Resolution: 1.6→36.221 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.17
RfactorNum. reflection% reflection
Rfree0.1809 3534 5.06 %
Rwork0.1442 --
obs0.1461 69798 92.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.11 Å2 / Biso mean: 17.689 Å2 / Biso min: 1.86 Å2
Refinement stepCycle: final / Resolution: 1.6→36.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 104 749 5695
Biso mean--23.21 26.86 -
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115056
X-RAY DIFFRACTIONf_angle_d1.1166844
X-RAY DIFFRACTIONf_chiral_restr0.06760
X-RAY DIFFRACTIONf_plane_restr0.009877
X-RAY DIFFRACTIONf_dihedral_angle_d13.2163065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.599-1.62090.20441100.19492265237581
1.6209-1.6440.23331120.17212469258185
1.644-1.66860.21451580.16022381253985
1.6686-1.69460.18821240.15792447257186
1.6946-1.72240.19981580.15362490264887
1.7224-1.75210.19481370.14792455259287
1.7521-1.7840.21111220.15392533265588
1.784-1.81830.17911220.15542498262088
1.8183-1.85540.20741170.16062572268989
1.8554-1.89570.19711250.16892528265389
1.8957-1.93980.20631430.15372580272390
1.9398-1.98830.19941400.15492557269791
1.9883-2.04210.20091330.15432670280393
2.0421-2.10220.18651310.13992701283294
2.1022-2.170.17211480.13732715286396
2.17-2.24760.1691410.1242790293198
2.2476-2.33760.16551520.127328392991100
2.3376-2.44390.16371600.134628803040100
2.4439-2.57270.18071450.139828452990100
2.5727-2.73390.20481760.14732814299099
2.7339-2.94490.18381410.14432807294898
2.9449-3.24110.17221680.14612781294999
3.2411-3.70960.1721500.141328763026100
3.7096-4.67220.14291550.126928843039100
4.6722-36.22990.19421660.15372887305399

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