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- PDB-7a5c: Crystal structure of spin labelled VcSiaP R125A bound to an artif... -

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Basic information

Entry
Database: PDB / ID: 7a5c
TitleCrystal structure of spin labelled VcSiaP R125A bound to an artificial peptide ligand.
ComponentsSialic acid-binding periplasmic protein SiaP
KeywordsTRANSPORT PROTEIN / TRAP / substrate binding protein / transporter
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / : / transmembrane transport / outer membrane-bounded periplasmic space / Sialic acid-binding periplasmic protein SiaP
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPeter, M.F. / Glaenzer, J. / Hagelueken, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)HA 6805/5-1 Germany
German Research Foundation (DFG)HA 6805/4-1 Germany
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates.
Authors: Peter, M.F. / Gebhardt, C. / Glaenzer, J. / Schneberger, N. / de Boer, M. / Thomas, G.H. / Cordes, T. / Hagelueken, G.
History
DepositionAug 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialic acid-binding periplasmic protein SiaP
B: Sialic acid-binding periplasmic protein SiaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0944
Polymers71,9102
Non-polymers1842
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-12 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.700, 118.700, 113.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Sialic acid-binding periplasmic protein SiaP


Mass: 35954.852 Da / Num. of mol.: 2 / Mutation: R125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: siaP, VC_1779 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KR64
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris (pH 8.5) and 1.26 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89429 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89429 Å / Relative weight: 1
ReflectionResolution: 2.2→59.35 Å / Num. obs: 46188 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 41.38 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.479 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3974 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
iMOSFLMdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAG

4mag


Resolution: 2.2→52.62 Å / SU ML: 0.3085 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3174
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 2335 5.06 %
Rwork0.1878 43796 -
obs0.1901 46131 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→52.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 12 227 5273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675193
X-RAY DIFFRACTIONf_angle_d0.98287049
X-RAY DIFFRACTIONf_chiral_restr0.05765
X-RAY DIFFRACTIONf_plane_restr0.0057918
X-RAY DIFFRACTIONf_dihedral_angle_d14.8672715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.33281290.31592555X-RAY DIFFRACTION100
2.25-2.290.34751370.28432572X-RAY DIFFRACTION100
2.29-2.350.32521350.28072567X-RAY DIFFRACTION100
2.35-2.410.31571330.27332562X-RAY DIFFRACTION100
2.41-2.470.29241350.27782605X-RAY DIFFRACTION100
2.47-2.540.32551460.25562522X-RAY DIFFRACTION100
2.54-2.630.29721430.2412560X-RAY DIFFRACTION100
2.63-2.720.26131420.24212568X-RAY DIFFRACTION100
2.72-2.830.29861380.23752618X-RAY DIFFRACTION100
2.83-2.960.30751290.23262560X-RAY DIFFRACTION100
2.96-3.110.27741760.22292531X-RAY DIFFRACTION100
3.11-3.310.25881370.20052581X-RAY DIFFRACTION100
3.31-3.560.29661190.18992605X-RAY DIFFRACTION100
3.56-3.920.19421350.1612585X-RAY DIFFRACTION100
3.92-4.490.19881450.1322558X-RAY DIFFRACTION100
4.49-5.650.19821180.14362637X-RAY DIFFRACTION100
5.66-52.620.15241380.15462610X-RAY DIFFRACTION98.96
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)
13.89764901570.0388102963306-3.356391292024.03577722542-2.658255070564.60002539933-0.3741156183230.6500349871080.0982520469528-0.9484941415970.1182005993910.07602737313320.0528351554142-0.7760504310740.05147991171720.7654073954190.111875886161-0.07167904247250.613407643805-0.04682239887180.474850474565-60.945257815614.7625984091-41.2778517085
23.798364547333.414922173512.079291335037.825636720742.614941442624.446068271990.2385727313180.507318239958-0.517669192449-0.641671051459-0.02125245543090.003853663427690.7319286164920.773099961047-0.199370489720.6069010783460.121251296858-0.09761167284410.331942042316-0.05060245377160.396178047062-65.67499746933.78748464514-26.5692669317
31.64314258259-0.7057853129340.5745051621393.0425240591-2.171673427193.828739400240.152842236335-0.041150801662-0.273403365042-0.00316962384940.2864630193740.5261487964110.212345960653-0.383136943264-0.371718690140.39361210158-0.0284625757392-0.06458846945230.2513700228110.07104078385870.494653682501-78.66515190349.62056465874-19.4757726638
40.6848654211530.5405110564730.715878055922.70885028825-0.9755952121661.948648211350.00764093184974-0.9546814143280.2029106966120.809741122715-0.09824700430630.609516396515-1.45328932134-0.1267315996251.150064272662.208664643830.08671540752870.04053263152650.0806872926859-0.4147219920830.252767757493-70.261409223120.71554691436.32380270642
51.58315406222-0.3394991493270.3383576752892.07132003804-1.787965777946.697653254290.0801779689148-0.06896417659410.1650295190340.4854623321730.1520098098290.201586838923-0.9059206884840.345007533413-0.1680935188220.633692778855-0.05671613429160.000953497928680.204526665041-0.01811155152450.447894448302-69.073011442611.3190236755-7.52103619886
68.999037618270.4235667022023.610701605078.644997062411.498068977076.92686286807-0.294136557964-1.10977440890.3624474883290.9927117272470.7151021503041.61101354405-1.0847510936-2.00656186982-0.4330455064950.787346584540.2877113815390.2932879094850.933010310160.3472604715720.834866709163-91.897918373213.1574788952-3.93569844597
78.90174109513-2.35785422161-4.019472129167.123720385095.150207703636.00852749942-0.495764483661-0.07102627733580.3585065283871.193152398370.150775959342-0.0664348532457-0.004819794887730.6874430783440.3422110635080.654538137597-0.153106688848-0.07577903766630.5297580662170.07188267301610.429828395574-57.858918354214.6294319866-14.8762890576
83.17699126639-2.220223856561.615618217267.88455135398-3.91864903214.981165783950.312078229166-0.360612069944-0.5468095118970.608943439324-0.03498507560650.2753247841180.686063176109-0.582783760034-0.2584438871050.580103020024-0.108108976392-0.07104204382360.3265252988690.03560433412060.361710834914-52.99482952533.88851262618-29.5219073191
91.417848387580.590058181540.7650812470712.912587340632.257711105873.730732340150.1370976662010.0692281347034-0.280265258731-0.02009034119230.309816002483-0.5252064200660.2144454377950.433659365924-0.3750702854040.4066836797870.0262203046021-0.04416049757040.255488667081-0.06462992176340.485598441728-40.03439694119.74890348432-36.4896247683
101.865058328280.2494841780240.6893441455372.321504663211.570244817477.137707825850.05339918548570.1469062619670.15316026243-0.6744179804030.250513818481-0.313203132931-1.17191449346-0.0035731787144-0.214802383940.773226167065-0.0001610720546470.063949395390.178599298448-0.001788803054920.489746376734-46.613408305812.6570375804-50.6220280305
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -16 through 1 )AA-16 - 11 - 18
22chain 'A' and (resid 2 through 30 )AA2 - 3019 - 49
33chain 'A' and (resid 31 through 129 )AA31 - 12950 - 149
44chain 'A' and (resid 130 through 149 )AA130 - 149150 - 169
55chain 'A' and (resid 150 through 277 )AA150 - 277170 - 297
66chain 'A' and (resid 278 through 299 )AA278 - 299298 - 319
77chain 'B' and (resid -16 through 1 )BC-16 - 11 - 18
88chain 'B' and (resid 2 through 30 )BC2 - 3019 - 50
99chain 'B' and (resid 31 through 129 )BC31 - 12951 - 149
1010chain 'B' and (resid 130 through 299 )BC130 - 299150 - 319

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