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- PDB-5dle: Crystal structure from a domain (Thr161-F265) from fructose-speci... -

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Basic information

Entry
Database: PDB / ID: 5dle
TitleCrystal structure from a domain (Thr161-F265) from fructose-specific iiabc component (Pts system) from Borrelia burgdorferi
ComponentsPts system, fructose-specific iiabc component
KeywordsTRANSFERASE / SSGCID / Borellia burgdorferi / Pts system / fructose-specific iiabc component / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity / carbohydrate:proton symporter activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Phosphotransferase system, IIA component fructose subfamily / Phosphotransferase system, fructose IIC component / Phosphotransferase system, fructose-specific IIB subunit / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. ...Phosphotransferase system, IIA component fructose subfamily / Phosphotransferase system, fructose IIC component / Phosphotransferase system, fructose-specific IIB subunit / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase/anion transporter / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Pts system, fructose-specific iiabc component
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure from a domain (Thr161-F265) from fructose-specific iiabc component (Pts system) from Borrelia burgdorferi
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pts system, fructose-specific iiabc component
B: Pts system, fructose-specific iiabc component
C: Pts system, fructose-specific iiabc component
D: Pts system, fructose-specific iiabc component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5979
Polymers50,2854
Non-polymers3125
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-29 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.950, 91.740, 80.670
Angle α, β, γ (deg.)90.000, 101.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pts system, fructose-specific iiabc component


Mass: 12571.346 Da / Num. of mol.: 4 / Fragment: UNP residues 161-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0408 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O51369
#2: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen G4: 20% PEG 3350, 200mM K/Na tartrate; BobuA.18902.a.B2.PS02426 at 22.3mg/ml, cryo 15% EG; tray 265189g4, puck nvm2-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 24, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 82616 / Num. obs: 80255 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 5.14 % / Biso Wilson estimate: 16.68 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.053 / Χ2: 0.998 / Net I/σ(I): 18.31 / Num. measured all: 412988
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.595.130.9260.5112.9129531612057540.56894
1.59-1.630.9470.4253.4929326587656350.47295.9
1.63-1.680.9490.3734.0428996578155580.41496.1
1.68-1.730.9660.2945.0728385565454440.32796.3
1.73-1.790.9750.2396.1527146541452340.26596.7
1.79-1.850.9880.1758.226330525050870.19596.9
1.85-1.920.9950.11611.5425520509349340.12996.9
1.92-20.9960.09314.3624653491047750.10497.3
2-2.090.9960.08117.0523446466745550.0997.6
2.09-2.190.9970.06421.3322356445443570.07197.8
2.19-2.310.9980.05324.3821419427641920.05998
2.31-2.450.9980.04926.1420465404739760.05598.2
2.45-2.620.9980.04229.8919262380037380.04798.4
2.62-2.830.9990.03932.8518003354635030.04398.8
2.83-3.10.9990.03436.816458327132250.03898.6
3.1-3.470.9990.03140.9114689292929040.03499.1
3.47-40.9990.02845.8513180264126100.03198.8
4-4.90.9990.02447.510972218621730.02799.4
4.9-6.930.9990.02445.648621173117120.02698.9
6.93-500.9990.02346.6842309708890.02691.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
PHENIX(1.10_2142: ???)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2r48, treated in MorDa

2r48


Resolution: 1.55→38.216 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 4041 5.04 %Random selection
Rwork0.1608 76144 --
obs0.1621 80185 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.78 Å2 / Biso mean: 24.3631 Å2 / Biso min: 9.5 Å2
Refinement stepCycle: final / Resolution: 1.55→38.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 21 532 3737
Biso mean--57.13 36.12 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123401
X-RAY DIFFRACTIONf_angle_d1.1674631
X-RAY DIFFRACTIONf_chiral_restr0.084562
X-RAY DIFFRACTIONf_plane_restr0.008603
X-RAY DIFFRACTIONf_dihedral_angle_d9.6332141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.56820.23421310.21572452258392
1.5682-1.58740.25311490.2192625277495
1.5874-1.60750.26771330.20542539267295
1.6075-1.62860.22241300.19152564269496
1.6286-1.65090.21891320.1862615274796
1.6509-1.67450.22311490.18212584273396
1.6745-1.69950.22981260.17322579270596
1.6995-1.72610.21361570.19052600275796
1.7261-1.75440.23181320.19672620275297
1.7544-1.78460.1921620.18992543270597
1.7846-1.81710.26331240.18012687281197
1.8171-1.8520.22811400.17422549268997
1.852-1.88980.20011210.16212639276097
1.8898-1.93090.16751200.15842648276897
1.9309-1.97580.17591260.15492629275597
1.9758-2.02520.18071420.16212620276298
2.0252-2.080.21021280.16782640276897
2.08-2.14120.18261560.15712641279798
2.1412-2.21030.16721560.15072639279598
2.2103-2.28930.17271480.15362596274498
2.2893-2.38090.17311350.15222701283698
2.3809-2.48930.16691420.15732653279598
2.4893-2.62050.19251510.15492637278899
2.6205-2.78460.1971340.16392686282099
2.7846-2.99950.19171510.16522659281099
2.9995-3.30120.19481570.16332691284899
3.3012-3.77850.16231440.14462685282999
3.7785-4.75910.15521460.13652715286199
4.7591-38.22740.17761190.16522708282797
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)
10.03170.1297-0.09160.2693-0.10820.12890.023-0.0062-0.0947-0.16110.03080.27880.1109-0.076100.14360.0093-0.04170.16560.0280.220223.84670.24153.1073
20.0103-0.0298-0.32721.3555-0.76480.74980.0440.03620.0455-0.13030.03580.22650.077-0.03030.01180.11950.0046-0.00830.11820.0110.163827.1453-5.403510.1232
30.26040.0346-0.16940.55760.00290.30160.20250.1250.0996-0.8122-0.1057-0.19350.57640.115-0.00010.30250.08410.03220.16530.00320.196534.3099-2.76420.1652
40.3165-0.41190.87511.4951-1.01991.3317-0.0821-0.06620.1330.1178-0.03550.0143-0.30770.0085-0.11830.15250.03130.00620.12930.02210.140127.63556.05499.4116
50.0837-0.1132-0.0480.3260.07630.0098-0.1131-0.11880.07470.36890.04050.0287-0.09570.01740.00010.23060.0348-0.01840.19520.00270.11749.5659-23.212535.3126
60.6279-0.43210.03070.6646-0.10410.08750.009-0.1027-0.0570.18660.0785-0.00360.08440.16880.00680.13380.0169-0.00550.13960.00550.136941.1296-16.430228.9505
70.6824-0.27350.02120.6492-0.0310.11480.05630.0340.27550.21290.0046-0.2096-0.08440.0230.01350.14080.0206-0.00850.17840.01320.149750.0294-18.252728.6914
80.1386-0.0907-0.17650.42660.02640.244-0.1245-0.18860.08450.31480.0848-0.0865-0.0303-0.01250.00750.21640.0441-0.06440.18990.02370.167553.7848-26.466232.5343
90.03910.0391-0.05580.1192-0.1060.03930.26020.3494-0.1657-0.0475-0.23360.10440.16040.3467-0.03690.16520.1001-0.04230.2792-0.04190.179847.7987-27.474519.3999
100.0932-0.2126-0.07820.1890.1590.15550.0159-0.0495-0.06440.00420.03060.09320.22180.086-0.01220.20690.0353-0.02190.16880.04040.180749.3173-31.757928.8344
110.1425-0.02330.31110.251-0.00850.30080.0347-0.0757-0.18630.1590.07550.21570.1344-0.17330.0860.20090.01070.02530.18970.07460.17739.4821-28.021933.6951
120.1188-0.1723-0.28880.76010.03320.2913-0.017-0.00190.10450.0668-0.049-0.07260.01510.13220.00010.1503-0.0219-0.01520.17130.00320.138743.5521-1.605934.0033
130.05480.1357-0.02890.2870.09920.24710.0516-0.0536-0.14060.0794-0.02-0.12070.140.162700.1278-0.00590.00950.1739-0.00520.160946.7649-6.942528.9719
140.03280.11390.05160.5370.16090.79190.03750.0127-0.10220.3696-0.1402-0.04810.1703-0.0093-0.05640.1921-0.04780.01220.1975-0.02720.149342.1445-4.487737.0695
150.0426-0.00360.02420.026-0.00150.0620.0711-0.5936-0.05630.6804-0.0903-0.24960.1009-0.0802-0.00780.4067-0.0953-0.03320.2632-0.03340.165545.07722.994847.3948
160.1170.0725-0.14350.24120.1420.2167-0.015-0.11160.210.1003-0.14060.0843-0.2733-0.10250.00820.1883-0.0459-0.00190.2049-0.04620.153540.15495.206133.58
170.35730.12170.34190.28010.08680.1659-0.02260.02790.10760.0425-0.0506-0.0234-0.21010.1129-0.05230.2018-0.06090.00290.1418-0.02370.1343.76475.758931.104
180.0910.00310.29560.2921-0.17190.30640.06290.1540.0666-0.2375-0.2789-0.1429-0.49740.0538-0.08780.2245-0.11140.00380.2935-0.04330.210851.23426.973429.9364
190.16490.1319-0.06990.3764-0.04620.023-0.10040.09260.1625-0.2784-0.031-0.0455-0.1044-0.02080.00030.1903-0.0026-0.01360.146-0.00920.110221.0956-23.18273.3347
200.32270.10360.14530.41580.08840.1430.00130.00020.067-0.09010.1367-0.1174-0.0411-0.02430.0050.1129-0.00430.02080.124-0.01270.148729.3357-16.24149.9373
210.7463-0.07510.1730.57650.12510.0940.0289-0.06590.1482-0.1677-0.00440.1412-0.07530.02320.01310.1197-0.0104-0.00190.1304-0.01570.134420.4227-18.328110.0525
220.12530.0762-0.1890.460.00260.297-0.00990.0508-0.0758-0.16940.09080.07150.1052-0.027800.156-0.0111-0.04760.1358-0.01370.186716.911-26.57196.0234
230.07750.213-0.02510.58590.0021-0.03260.3332-0.4747-0.34480.3879-0.3483-0.3829-0.0856-0.40250.00170.1844-0.0494-0.03020.34250.0260.14822.1708-29.113618.8103
240.05710.0025-0.04570.0230.07630.0618-0.07710.0390.05410.0960.1429-0.00250.3490.007200.2068-0.0118-0.01030.1192-0.02310.182716.7073-32.8339.1838
250.06940.05390.02740.08620.03330.06670.02970.1656-0.22830.02790.1135-0.27650.08070.13320.04560.12550.02030.00030.1456-0.05650.193532.6059-25.928610.3497
260.3138-0.11770.47130.3130.0730.47890.0708-0.1403-0.3612-0.21710.0526-0.30950.15710.07190.17150.2113-0.00210.0240.222-0.08390.227429.1358-29.96532.7498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 171 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 172 through 202 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 218 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 265 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 162 through 171 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 172 through 192 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 193 through 212 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 213 through 226 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 227 through 232 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 233 through 244 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 245 through 265 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 162 through 176 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 177 through 192 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 193 through 212 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 213 through 218 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 219 through 232 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 233 through 251 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 252 through 265 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 162 through 171 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 172 through 192 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 193 through 212 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 213 through 226 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 227 through 232 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 233 through 239 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 240 through 251 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 252 through 265 )D0

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