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- PDB-7vew: Crystal structure of bacterial chemotaxis-dependent pectin-bindin... -

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Basic information

Entry
Database: PDB / ID: 7vew
TitleCrystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with unsaturated trigalacturonic acid
ComponentsSPH1118
KeywordsSUGAR BINDING PROTEIN / pectin-binding protein / chemotaxis / gram-negative bacteria
Function / homologyDipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Roll / Alpha Beta / L(+)-TARTARIC ACID
Function and homology information
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsAnamizu, K. / Takase, R. / Hio, M. / Watanebe, D. / Mikami, B. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Sci Rep / Year: 2022
Title: Substrate size-dependent conformational changes of bacterial pectin-binding protein crucial for chemotaxis and assimilation.
Authors: Anamizu, K. / Takase, R. / Hio, M. / Watanabe, D. / Mikami, B. / Hashimoto, W.
History
DepositionSep 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPH1118
B: SPH1118
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,36313
Polymers140,1012
Non-polymers2,26211
Water8,629479
1
A: SPH1118
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0435
Polymers70,0511
Non-polymers9934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23500 Å2
MethodPISA
2
B: SPH1118
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3208
Polymers70,0511
Non-polymers1,2697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.687, 83.657, 148.521
Angle α, β, γ (deg.)90.000, 101.036, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein SPH1118


Mass: 70050.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D- ...2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 512.373 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2112A-1a_1-5][a21eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-4-deoxy-GlcpA]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 488 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 22% PEG3000 0.15 M Potassium sodium tartrate 0.1 M HEPES 23.4 mM Unsaturated trigalacturonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.6 Å / Num. obs: 108404 / % possible obs: 99.5 % / Redundancy: 5.77 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 0.645 / Num. unique obs: 17122

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VEV

7vev


Resolution: 1.92→48.591 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE / ESU R: 0.171 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2324 5288 5 %
Rwork0.2096 100473 -
all0.211 --
obs-105761 99.894 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.749 Å2
Baniso -1Baniso -2Baniso -3
1-5.528 Å20 Å21.119 Å2
2---3.394 Å2-0 Å2
3----2.389 Å2
Refinement stepCycle: LAST / Resolution: 1.92→48.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9692 0 152 479 10323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01310103
X-RAY DIFFRACTIONr_bond_other_d0.0340.0179535
X-RAY DIFFRACTIONr_angle_refined_deg1.731.65813716
X-RAY DIFFRACTIONr_angle_other_deg2.2111.58621989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28251220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88522.788513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.902151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6811558
X-RAY DIFFRACTIONr_chiral_restr0.0980.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211364
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022334
X-RAY DIFFRACTIONr_nbd_refined0.2270.22026
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.29324
X-RAY DIFFRACTIONr_nbtor_refined0.1840.25100
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24721
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2445
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.211
X-RAY DIFFRACTIONr_nbd_other0.3730.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0840.28
X-RAY DIFFRACTIONr_mcbond_it1.9663.6264880
X-RAY DIFFRACTIONr_mcbond_other1.9633.6264879
X-RAY DIFFRACTIONr_mcangle_it2.4025.4236100
X-RAY DIFFRACTIONr_mcangle_other2.4055.4236101
X-RAY DIFFRACTIONr_scbond_it2.7573.7565223
X-RAY DIFFRACTIONr_scbond_other2.7563.7565223
X-RAY DIFFRACTIONr_scangle_it3.5095.5437616
X-RAY DIFFRACTIONr_scangle_other3.5095.5427617
X-RAY DIFFRACTIONr_lrange_it3.7541.99211485
X-RAY DIFFRACTIONr_lrange_other3.75241.92911414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.92-1.970.3553850.33773070.33876960.5170.51999.9480.318
1.97-2.0240.3023790.29272090.29375900.6140.59499.97360.266
2.024-2.0820.313700.2770330.27274070.6120.64799.9460.237
2.082-2.1460.3073610.25468480.25772120.7160.73699.95840.221
2.146-2.2160.2873470.23365970.23669460.8160.83199.97120.203
2.216-2.2940.2613350.23163660.23267070.8350.84799.91050.201
2.294-2.380.2653250.2261730.22264990.8780.88799.98460.193
2.38-2.4770.2653130.21559490.21762640.8890.90499.96810.191
2.477-2.5870.2382980.20956670.2159670.9110.91899.96650.188
2.587-2.7130.2612870.21354400.21557350.9160.92699.86050.194
2.713-2.8590.2472750.21852340.2255100.9090.92299.98180.203
2.859-3.0320.2282590.21449150.21551760.9330.93199.96140.205
3.032-3.2410.2552430.22646190.22848660.9140.91999.91780.222
3.241-3.4990.232260.2242960.2245300.9320.93299.82340.221
3.499-3.8310.2282080.20239580.20341870.9430.94799.49840.208
3.831-4.280.1871890.17235840.17337760.9620.96599.92060.187
4.28-4.9360.1641680.15431880.15533640.970.96899.76220.181
4.936-6.0290.2061430.1827120.18128590.9540.95799.86010.206
6.029-8.4620.1721120.18621280.18622440.9660.95999.82170.223
8.462-48.5910.189640.17712160.17712940.9580.95698.91810.218

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