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

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Basic information

Entry
Database: PDB / ID: 7vev
TitleCrystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with MES
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
Function and homology information
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 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

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Assembly

Deposited unit
A: SPH1118
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6829
Polymers70,0511
Non-polymers6318
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-9 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.060, 54.210, 57.012
Angle α, β, γ (deg.)75.859, 66.897, 87.947
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SPH1118


Mass: 70050.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG6000 0.2 M Calcium chloride 0.1 M MES

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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: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.498→50 Å / Num. obs: 79704 / % possible obs: 99.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 27.4
Reflection shellResolution: 1.5→1.52 Å / Rmerge(I) obs: 0.139 / Num. unique obs: 10578

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IPW

5ipw


Resolution: 1.498→26.133 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1879 3892 4.883 %
Rwork0.1673 75811 -
all0.168 --
obs-79703 94.765 %
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: 11.403 Å2
Baniso -1Baniso -2Baniso -3
1--0.478 Å2-0.01 Å2-0.078 Å2
2--0.162 Å2-0.26 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.498→26.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 30 507 5409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135098
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174856
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6476935
X-RAY DIFFRACTIONr_angle_other_deg2.2581.5811210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03222.759261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23115883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6631530
X-RAY DIFFRACTIONr_chiral_restr0.1240.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025782
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021190
X-RAY DIFFRACTIONr_nbd_refined0.2170.2972
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.24767
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22565
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2314
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2950.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.213
X-RAY DIFFRACTIONr_nbd_other0.2280.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.238
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0550.22
X-RAY DIFFRACTIONr_mcbond_it1.2190.9742481
X-RAY DIFFRACTIONr_mcbond_other1.2180.9742480
X-RAY DIFFRACTIONr_mcangle_it1.8971.4663109
X-RAY DIFFRACTIONr_mcangle_other1.8971.4673110
X-RAY DIFFRACTIONr_scbond_it1.9421.2222617
X-RAY DIFFRACTIONr_scbond_other1.9421.2222615
X-RAY DIFFRACTIONr_scangle_it3.1321.7283819
X-RAY DIFFRACTIONr_scangle_other3.1321.7283820
X-RAY DIFFRACTIONr_lrange_it4.28212.4725868
X-RAY DIFFRACTIONr_lrange_other4.17512.2285792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.498-1.5370.2062900.1945232X-RAY DIFFRACTION88.5362
1.537-1.5790.2132900.185378X-RAY DIFFRACTION93.8877
1.579-1.6240.1972900.1765291X-RAY DIFFRACTION94.2737
1.624-1.6740.192860.1765156X-RAY DIFFRACTION94.7918
1.674-1.7290.1912740.1764954X-RAY DIFFRACTION94.7101
1.729-1.790.1962370.174854X-RAY DIFFRACTION95.0878
1.79-1.8570.2122270.1714722X-RAY DIFFRACTION95.6329
1.857-1.9330.1872140.1684558X-RAY DIFFRACTION95.1925
1.933-2.0190.172010.1694372X-RAY DIFFRACTION95.87
2.019-2.1170.2162100.1674173X-RAY DIFFRACTION95.6778
2.117-2.2320.1832030.1663949X-RAY DIFFRACTION95.8891
2.232-2.3670.21910.1613765X-RAY DIFFRACTION95.7869
2.367-2.530.1631810.1533491X-RAY DIFFRACTION96.0754
2.53-2.7320.1911920.1793212X-RAY DIFFRACTION93.8776
2.732-2.9920.1981520.1723031X-RAY DIFFRACTION96.0761
2.992-3.3440.1871210.1592745X-RAY DIFFRACTION96.661
3.344-3.8580.1721200.1472435X-RAY DIFFRACTION96.5244
3.858-4.7190.126930.1412054X-RAY DIFFRACTION96.5812
4.719-6.6470.216780.1951596X-RAY DIFFRACTION96.2069

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