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- PDB-35yt: Re-refined Phosphate-Binding Protein (PstS2) from Xanthomonas cit... -

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Basic information

Entry
Database: PDB / ID: 35yt
TitleRe-refined Phosphate-Binding Protein (PstS2) from Xanthomonas citri pv. citri A306 Bound to Phosphate
ComponentsPhosphate-binding protein PstS
KeywordsTRANSPORT PROTEIN / SBP / ABC Transporter
Function / homology
Function and homology information


phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / : / PBP domain / PBP superfamily domain
Similarity search - Domain/homology
IODIDE ION / PHOSPHATE ION / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesXanthomonas citri subsp. citri 306 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsSantos, L.S. / Balan, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
Citation
Journal: To Be Published
Title: Re-refined Phosphate-Binding Protein (PstS2) from Xanthomonas citri pv. citri A306 Bound to Phosphate
Authors: Santos, L.S. / Balan, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#2: Journal: PLoS One / Year: 2017
Title: Structural features of PhoX, one of the phosphate-binding proteins from Pho regulon of Xanthomonas citri.
Authors: Pegos, V.R. / Santos, R.M.L. / Medrano, F.J. / Balan, A.
History
DepositionMay 23, 2026Deposition site: RCSB / Processing site: RCSB
SupersessionJun 10, 2026ID: 5I84
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphate-binding protein PstS
B: Phosphate-binding protein PstS
C: Phosphate-binding protein PstS
D: Phosphate-binding protein PstS
E: Phosphate-binding protein PstS
F: Phosphate-binding protein PstS
G: Phosphate-binding protein PstS
H: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,22073
Polymers282,9198
Non-polymers6,30165
Water1267
1
A: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,44112
Polymers35,3651
Non-polymers1,07711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1259
Polymers35,3651
Non-polymers7608
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0628
Polymers35,3651
Non-polymers6977
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1579
Polymers35,3651
Non-polymers7928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0308
Polymers35,3651
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1259
Polymers35,3651
Non-polymers7608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9357
Polymers35,3651
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,34711
Polymers35,3651
Non-polymers98210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.556, 115.643, 133.323
Angle α, β, γ (deg.)90.000, 90.331, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 29 through 339 or resid 511 or resid 513 through 514))
d_2ens_1(chain "B" and (resid 29 through 339 or resid 512 or resid 514 through 515))
d_3ens_1(chain "C" and (resid 29 through 339 or resid 407 or resid 409 through 411))
d_4ens_1(chain "D" and (resid 29 through 339 or resid 405 or resid 407 through 408))
d_5ens_1(chain "E" and (resid 29 through 339 or resid 404 or resid 406 through 407))
d_6ens_1(chain "F" and (resid 29 through 339 or resid 402 or resid 404 through 405))
d_7ens_1(chain "G" and (resid 29 through 504 or resid 506 through 507))
d_8ens_1(chain "H" and (resid 29 through 339 or resid 406 or resid 521 through 522))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRPROPROAA29 - 33924 - 334
d_12PO4PO4PO4PO4AL404
d_13PO4PO4PO4PO4AN406
d_14PO4PO4PO4PO4AO407
d_21THRTHRPROPROBB29 - 33924 - 334
d_22PO4PO4PO4PO4BW404
d_23PO4PO4PO4PO4BY406
d_24PO4PO4PO4PO4BZ407
d_31THRTHRPROPROCC29 - 33924 - 334
d_32PO4PO4PO4PO4CCA402
d_33PO4PO4PO4PO4CEA404
d_34PO4PO4PO4PO4CFA405
d_41THRTHRPROPRODD29 - 33924 - 334
d_42PO4PO4PO4PO4DKA403
d_43PO4PO4PO4PO4DMA405
d_44PO4PO4PO4PO4DNA406
d_51THRTHRPROPROEE29 - 33924 - 334
d_52PO4PO4PO4PO4ETA404
d_53PO4PO4PO4PO4DPA408
d_54PO4PO4PO4PO4EVA406
d_61THRTHRPROPROFF29 - 33924 - 334
d_62PO4PO4PO4PO4FZA403
d_63PO4PO4PO4PO4FBB405
d_64PO4PO4PO4PO4FCB406
d_71THRTHRPROPROGG29 - 33924 - 334
d_72PO4PO4PO4PO4GGB402
d_73PO4PO4PO4PO4AS411
d_74PO4PO4PO4PO4GIB404
d_81THRTHRPROPROHH29 - 33924 - 334
d_82PO4PO4PO4PO4HPB405
d_83PO4PO4PO4PO4HRB407
d_84PO4PO4PO4PO4HSB408

NCS oper:
IDCodeMatrixVector
1given(0.91021770390011, 0.19201872418345, 0.36692307241407), (-0.23363588566631, -0.49344935099487, 0.83780786039023), (0.34193274841076, -0.84831394398872, -0.40428387056444)-11.488800721719, 22.067914471394, 137.7500054113
2given(0.99606799864402, 0.044592904629397, -0.076550734379273), (0.04934801179076, -0.99689305902243, 0.061392203130344), (-0.073575239106587, -0.064928435447129, -0.99517384534603)2.3601846311972, 122.10194188242, 211.17831955226
3given(-0.88976477950682, -0.2955328112161, -0.34782034823151), (0.15568696599247, 0.51983925253605, -0.839957570442), (0.42904569193646, -0.80151575718602, -0.41652405118227)179.33019167863, 54.121020702152, 196.78578468111
4given(0.65490702797177, 0.75566655100917, -0.0080528503702314), (-0.7555979205323, 0.65459011632823, -0.024157029880701), (-0.012983343191951, 0.0219053256379, 0.99967574218256)-43.283701388013, 36.429942782991, 40.598563819344
5given(-0.78583877775153, -0.49808628602667, 0.36656168246851), (0.51488631185432, -0.19862073664661, 0.83393158522688), (-0.34256313468767, 0.84407337041641, 0.41254168771996)132.44360221627, -41.59595378277, 36.624354329431
6given(0.60925244029976, 0.78792035711593, -0.089403438586501), (0.78821790864225, -0.61406793323754, -0.040411655064016), (-0.086740950446827, -0.045848491923774, -0.99517532289738)-36.5274461921, 93.67919231741, 168.60972804898
7given(0.71833767275291, 0.56986533640297, -0.3990544903522), (-0.54692517444497, 0.10808115998407, -0.83017547326745), (-0.42995795313294, 0.81459926419241, 0.38931246745373)28.813768444187, 124.30960631289, 112.5080917837

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Components

#1: Protein
Phosphate-binding protein PstS


Mass: 35364.879 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri subsp. citri 306 (bacteria)
Gene: phoX, XAC1578 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAI8ERC0
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 61 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium iodide 20% PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.98→17.06 Å / Num. obs: 49489 / % possible obs: 98.62 % / Redundancy: 2.8 % / Biso Wilson estimate: 48.25 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 2.98→3.04 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 2176

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→17.06 Å / SU ML: 0.3835 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.6168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2733 2491 5.03 %
Rwork0.2503 46998 -
obs0.2515 49489 98.62 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.46 Å2
Refinement stepCycle: LAST / Resolution: 2.98→17.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18673 0 309 7 18989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005619385
X-RAY DIFFRACTIONf_angle_d0.792626437
X-RAY DIFFRACTIONf_chiral_restr0.05252873
X-RAY DIFFRACTIONf_plane_restr0.00573365
X-RAY DIFFRACTIONf_dihedral_angle_d10.94646711
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.9666461923704
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.7449096566874
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS2.6972040440781
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS3.0480593710651
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS3.6803079990512
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS3.0463687607314
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS3.5736879601394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.040.3211070.31792069X-RAY DIFFRACTION77.83
3.04-3.10.31561430.29982620X-RAY DIFFRACTION99.93
3.1-3.170.29291260.30482639X-RAY DIFFRACTION99.96
3.17-3.240.30591240.29652648X-RAY DIFFRACTION99.96
3.24-3.320.33231400.30492634X-RAY DIFFRACTION100
3.32-3.410.29791210.29052658X-RAY DIFFRACTION99.96
3.41-3.510.33641570.2892614X-RAY DIFFRACTION99.96
3.51-3.630.32991150.2792682X-RAY DIFFRACTION100
3.63-3.750.31091600.26422595X-RAY DIFFRACTION99.96
3.75-3.90.2751320.25292647X-RAY DIFFRACTION99.82
3.9-4.080.26171320.24862654X-RAY DIFFRACTION99.86
4.08-4.290.2561540.23652648X-RAY DIFFRACTION99.93
4.29-4.550.22361380.21432628X-RAY DIFFRACTION100
4.55-4.90.23811530.21712650X-RAY DIFFRACTION99.79
4.9-5.380.26341410.2192631X-RAY DIFFRACTION99.86
5.38-6.120.28171510.2422638X-RAY DIFFRACTION99.75
6.12-7.60.26331610.2422645X-RAY DIFFRACTION99.89
7.6-17.060.2111360.20272698X-RAY DIFFRACTION98.88

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