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

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Basic information

Entry
Database: PDB / ID: 5iga
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, Triple Surface Mutant K158A_K223A_K313A) in complex with co-purified parahydroxybenzoate
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 / DI(HYDROXYETHYL)ETHER / P-HYDROXYBENZOIC ACID
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 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, Triple Surface Mutant K158A_K223A_K313A) in complex with co-purified parahydroxybenzoate
Authors: Vetting, M.W. / Al Obaidi, N.F. / Hogle, S.L. / Dupont, C.L. / Almo, S.C.
History
DepositionFeb 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2748
Polymers37,4831
Non-polymers7917
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.830, 84.470, 46.069
Angle α, β, γ (deg.)90.000, 113.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRAP TRANSPORTER SOLUTE BINDING PROTEIN


Mass: 37482.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gene discovered by metagenome sequencing of ocean samples was synthesized by gibson synthesis. Surface mutants were prepared to potentially enhancing crystallization.
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 1.9 Å3/Da / Density % sol: 35.27 % / Mosaicity: 0.671 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3-(3-hydroxyphenyl)propionic acid); Reservoir (MCSG2 (H4) 0.2 M Ammonium Acetate, 0.1 M Tris pH 8.5 25 %(w/v) PEG 3350); Cryoprotection (20% ...Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3-(3-hydroxyphenyl)propionic acid); Reservoir (MCSG2 (H4) 0.2 M Ammonium Acetate, 0.1 M Tris pH 8.5 25 %(w/v) PEG 3350); Cryoprotection (20% diethylene glycol, 80% reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 15, 2016 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 49010 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.29 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.055 / Rrim(I) all: 0.126 / Χ2: 0.975 / Net I/av σ(I): 11.784 / Net I/σ(I): 20.4 / Num. measured all: 164361
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.4820.16522970.9340.1390.2170.99692.6
1.48-1.52.10.14523320.9390.1210.190.90794
1.5-1.532.10.12923840.9530.1070.1680.85695.3
1.53-1.562.20.12223650.9510.1010.1590.82296.3
1.56-1.62.30.11124350.9620.0890.1430.78197.1
1.6-1.632.30.10424240.9690.0820.1330.76698
1.63-1.672.40.09624270.970.0740.1220.68499.1
1.67-1.722.50.08924860.9740.0690.1130.63198.9
1.72-1.772.60.08324610.9770.0630.1050.5799.1
1.77-1.832.70.07724720.9810.0560.0960.52699.4
1.83-1.892.70.07224780.9860.0510.0890.51299.4
1.89-1.972.90.08524790.9810.0560.1020.73599.6
1.97-2.063.30.10624680.9760.0640.1241.03399.5
2.06-2.173.50.11424840.9740.0640.1311.18499.5
2.17-2.340.13124650.9770.0670.1481.43599.6
2.3-2.484.70.15125010.9720.0710.1671.48999.4
2.48-2.735.60.15324780.9680.070.1681.41199.7
2.73-3.1260.13225170.9760.0590.1451.084100
3.12-3.945.90.10825090.9830.0490.1190.929100
3.94-10050.08625480.9860.0420.0960.53199.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I5P

5i5p


Resolution: 1.45→42.338 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.85
RfactorNum. reflection% reflection
Rfree0.1429 2523 5.19 %
Rwork0.1196 --
obs0.1208 48637 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.86 Å2 / Biso mean: 17.3391 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: final / Resolution: 1.45→42.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 110 478 2996
Biso mean--19.65 29 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082544
X-RAY DIFFRACTIONf_angle_d1.053440
X-RAY DIFFRACTIONf_chiral_restr0.075381
X-RAY DIFFRACTIONf_plane_restr0.008440
X-RAY DIFFRACTIONf_dihedral_angle_d17.846940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4459-1.47370.20881070.16282275238287
1.4737-1.50380.17451280.14862443257193
1.5038-1.53650.16211350.12952515265095
1.5365-1.57230.15751280.12332488261696
1.5723-1.61160.13221590.11832529268897
1.6116-1.65510.14431310.1172607273898
1.6551-1.70390.13891500.11172590274098
1.7039-1.75890.13511520.11152550270298
1.7589-1.82170.15471560.11142569272598
1.8217-1.89470.13471390.11792602274198
1.8947-1.98090.16771330.11842581271498
1.9809-2.08530.12241460.10932600274699
2.0853-2.2160.14421330.10882608274199
2.216-2.3870.12561410.11392589273099
2.387-2.62720.11891410.11712608274999
2.6272-3.00730.14551540.122926482802100
3.0073-3.78850.14521580.124826172775100
3.7885-42.35580.15181320.12292695282799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1983-0.0351-0.09050.17710.05070.34260.00480.049-0.0571-0.0737-0.0481-0.11220.01520.0134-0.12680.09840.00560.0160.10830.01580.139116.0964-11.43333.3877
20.0042-0.0352-0.02540.04710.03240.0102-0.02710.0042-0.0238-0.0082-0.00480.0260.0306-0.0326-00.1075-0.00230.00720.1058-0.00740.10752.5176-13.64368.2195
30.0623-0.0605-0.15750.4958-0.0190.1748-0.0245-0.01520.02340.06010.02270.0144-0.0138-0.0096-0.00020.066-0.00170.00420.06160.0010.0551-0.16253.080315.0231
40.0487-0.0374-0.03020.02160.00520.0250.0070.01750.07260.0225-0.02410.03560.0483-0.0600.0967-0.00250.00260.13760.00780.1447-11.77424.044912.5665
50.0688-0.0981-0.01810.1895-0.18710.10490.01150.0156-0.0193-0.0205-0.00380.01410.0016-0.0364-00.1043-0.0004-0.00640.1102-0.00290.1044-3.87246.70951.918
60.13130.0385-0.10570.1516-0.00470.3343-0.0082-0.0261-0.00510.0545-0.0671-0.0956-0.00930.0101-0.12160.0893-0.0011-0.01240.09860.01890.129717.2583-13.538615.469
70.0549-0.07340.03090.07250.02810.09860.02270.05670.0750.0127-0.0609-0.0982-0.03330.0789-0.00490.10910.00050.00030.11530.00940.11917.348410.63834.1242
80.0455-0.0511-0.07060.0330.05390.0929-0.07420.02120.00310.04290.15040.156-0.0652-0.186500.1710.00580.02830.14620.00690.1381-8.71829.618723.3289
90.181-0.0312-0.01540.11010.0650.002-0.0579-0.2932-0.05910.22970.0025-0.1228-0.00440.1516-0.00820.1545-0.0019-0.01180.1428-0.0090.12535.55046.790427.5811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 65 )A23 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 95 )A66 - 95
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 172 )A96 - 172
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 190 )A173 - 190
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 237 )A191 - 237
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 264 )A238 - 264
7X-RAY DIFFRACTION7chain 'A' and (resid 265 through 297 )A265 - 297
8X-RAY DIFFRACTION8chain 'A' and (resid 298 through 322 )A298 - 322
9X-RAY DIFFRACTION9chain 'A' and (resid 323 through 342 )A323 - 342

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