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- PDB-8dte: Crystal Structure of a toluene tolerance periplasmic transport pr... -

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Basic information

Entry
Database: PDB / ID: 8dte
TitleCrystal Structure of a toluene tolerance periplasmic transport protein from Neisseria gonorrhoeae
ComponentsPeriplasmic transport protein
KeywordsTRANSPORT PROTEIN / SSGCID / Periplasmic transport / toluene tolerance / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyTgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / Periplasmic transport protein
Function and homology information
Biological speciesNeisseria gonorrhoeae NCCP11945 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of a toluene tolerance periplasmic transport protein from Neisseria gonorrhoeae
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1104
Polymers20,0151
Non-polymers953
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.760, 51.760, 167.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-201-

MG

21A-323-

HOH

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Components

#1: Protein Periplasmic transport protein


Mass: 20014.896 Da / Num. of mol.: 1 / Fragment: NegoA.18500.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae NCCP11945 (bacteria)
Strain: NCCP11945 / Gene: NGK_2593 / Plasmid: NegoA.18500.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4RRD5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: [Target: NegoA.18500.a.B2.PS38078 - 50mg/mL] [Barcode: 321600a1] [Pin: mnd9-2] [Crystallization: sparse screen - Morpheus A1 - 10% (w/v) PEG 20000, 20% (v/v) PEG MME 550, 0.03M of each ...Details: [Target: NegoA.18500.a.B2.PS38078 - 50mg/mL] [Barcode: 321600a1] [Pin: mnd9-2] [Crystallization: sparse screen - Morpheus A1 - 10% (w/v) PEG 20000, 20% (v/v) PEG MME 550, 0.03M of each divalent cation(0.3M Magnesium chloride, 0.3M Calcium chloride), 0.1M MES/imidazole pH 6.5, 14C, 0.2:0.2 drop ratio] [Cryo: direct]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 3, 2022 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.2→37.97 Å / Num. obs: 12332 / % possible obs: 99.9 % / Redundancy: 11.527 % / Biso Wilson estimate: 38.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.058 / Χ2: 0.91 / Net I/σ(I): 30.87 / Num. measured all: 142146
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.2611.8210.5445.28105098898890.9620.568100
2.26-2.3211.9040.456.29102738638630.9760.47100
2.32-2.3911.8630.3817.2897168198190.980.398100
2.39-2.4611.9060.3348.23100498448440.9820.349100
2.46-2.5411.8270.26310.3792967867860.9860.275100
2.54-2.6311.840.20912.891297717710.9930.218100
2.63-2.7311.8360.17814.8688657497490.9940.186100
2.73-2.8411.7930.14217.9383857127110.9970.14899.9
2.84-2.9711.7340.10823.3181556956950.9980.113100
2.97-3.1111.6270.0927.7476276576560.9980.09499.8
3.11-3.2811.6310.06535.9575256486470.9990.06899.8
3.28-3.4811.5420.04747.5269376016010.9990.049100
3.48-3.7211.3990.0453.3666805865860.9990.042100
3.72-4.0211.30.03263.9595552752710.034100
4.02-4.411.1740.02774.18550949449310.02899.8
4.4-4.9211.0040.02775.7250184564560.9990.028100
4.92-5.6810.8260.02771.73448241441410.028100
5.68-6.9610.3690.02771.32365035235210.028100
6.96-9.849.9010.0283.34289129229210.021100
9.84-37.978.260.01979.44149518618110.0297.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.2→37.97 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 1245 10.15 %
Rwork0.1995 11025 -
obs0.2033 12270 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.16 Å2 / Biso mean: 47.4292 Å2 / Biso min: 25.37 Å2
Refinement stepCycle: final / Resolution: 2.2→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 3 94 1391
Biso mean--46.09 52.15 -
Num. residues----172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.290.22881450.213611841329100
2.29-2.390.27881330.206611891322100
2.39-2.520.23021440.199311961340100
2.52-2.680.22961490.21211731322100
2.68-2.880.30621120.231712521364100
2.88-3.170.25361370.208612011338100
3.17-3.630.25361290.202112411370100
3.63-4.570.20361270.1731264139199
4.57-37.970.22991690.20331325149498
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)
19.7748-3.9666-1.08476.7491-0.43124.2927-0.01870.84740.0673-0.60990.05030.3875-0.08190.1534-0.01920.2686-0.1021-0.07320.46830.03460.3199-7.211823.1145-14.7414
25.8458-1.23720.67294.4111-2.78662.40220.2811-0.17250.67110.3015-0.00390.2273-1.1056-0.4484-0.09070.31670.01250.03310.3866-0.05050.2958-12.632123.77688.0695
33.92070.20282.04364.42170.41752.7643-0.02980.2903-0.0054-0.14640.00270.14010.59471.1907-0.11140.22450.00560.04070.42240.04640.3179-7.635615.87660.9298
44.99-0.4876-1.13175.30690.54348.52160.38540.51520.5714-0.6663-0.11610.91420.2628-1.7586-0.41490.4467-0.0211-0.17490.43280.16820.6393-20.522327.2329-12.3039
53.5515-0.60662.24395.87760.29983.26370.1422-0.0567-0.1757-1.5073-0.2181-0.5781-0.4304-0.2979-0.06550.3105-0.0650.06590.54980.09020.3584-19.688522.829-11.0577
61.7829-1.94331.54842.4956-2.87698.4836-0.0637-0.1315-0.00310.05310.09670.17510.341-0.3574-0.00950.1901-0.02110.02170.3160.00860.2494-14.324616.73445.3322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 61 )A23 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 80 )A62 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 105 )A81 - 105
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 133 )A106 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 149 )A134 - 149
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 194 )A150 - 194

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