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- PDB-6uxt: Crystal structure of unknown function protein yfdX from Shigella ... -

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Basic information

Entry
Database: PDB / ID: 6uxt
TitleCrystal structure of unknown function protein yfdX from Shigella flexneri
ComponentsYfdX protein
KeywordsSTRUCTURAL GENOMICS / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


YfdX protein domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2140 / Uncharacterised protein family YfdX / YfdX protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Four Helix Bundle (Hemerythrin (Met), subunit A) / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / YfdX family protein
Similarity search - Component
Biological speciesShigella flexneri 2a str. 2457T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsChang, C. / Skarina, T. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of unknown function protein yfdX from Shigella flexneri
Authors: Chang, C. / Skarina, T. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: YfdX protein
B: YfdX protein
C: YfdX protein
D: YfdX protein
E: YfdX protein
F: YfdX protein
G: YfdX protein
H: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,02812
Polymers162,3838
Non-polymers6454
Water13,565753
1
A: YfdX protein
B: YfdX protein
C: YfdX protein
D: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4486
Polymers81,1914
Non-polymers2562
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-57 kcal/mol
Surface area27670 Å2
MethodPISA
2
E: YfdX protein
F: YfdX protein
G: YfdX protein
H: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5806
Polymers81,1914
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-49 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.579, 92.920, 93.469
Angle α, β, γ (deg.)97.350, 98.440, 95.460
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
YfdX protein


Mass: 20297.846 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria)
Gene: yfdX, / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Y2P124
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG3350, 0.2M ammonium citrate, 50mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.797→50 Å / Num. obs: 143645 / % possible obs: 91.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.037 / Rrim(I) all: 0.073 / Χ2: 0.861 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.50.47771830.8230.2960.5620.44691.4
1.83-1.863.60.40672150.8830.2480.4770.47191.6
1.86-1.93.60.3471560.9080.2060.3980.49891.1
1.9-1.943.70.27772000.9420.1670.3240.5291.6
1.94-1.983.70.24370290.9520.1460.2840.55389.4
1.98-2.033.70.269470.9670.120.2340.57589.2
2.03-2.083.60.16666690.9730.10.1950.65583.8
2.08-2.133.70.1572640.9780.090.1750.65793.1
2.13-2.23.70.12873250.9840.0770.1490.72894
2.2-2.273.70.11373320.9850.0680.1320.81492.3
2.27-2.353.80.171510.9860.060.1170.79991
2.35-2.443.70.08971150.9890.0530.1040.84790.7
2.44-2.553.70.08168470.9910.0480.0940.89787.4
2.55-2.693.80.07474630.9910.0440.0860.91594.7
2.69-2.863.80.06773840.9930.040.0780.96493.7
2.86-3.083.80.06272420.9940.0360.0721.11892.5
3.08-3.393.80.05570370.9940.0330.0641.389.7
3.39-3.883.80.04975060.9960.0290.0571.39195.4
3.88-4.883.80.04670940.9960.0270.0531.44290.3
4.88-503.80.04574860.9970.0270.0531.39895.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A02

6a02


Resolution: 1.797→43.517 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.91
RfactorNum. reflection% reflection
Rfree0.2003 7201 5.01 %
Rwork0.1701 --
obs0.1716 143610 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.5 Å2 / Biso mean: 32.3239 Å2 / Biso min: 15.35 Å2
Refinement stepCycle: final / Resolution: 1.797→43.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10010 0 42 753 10805
Biso mean--56.44 36.25 -
Num. residues----1306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.797-1.81690.36592320.2962414083
1.8169-1.83830.32112550.2729455191
1.8383-1.86070.26892400.2398455492
1.8607-1.88430.24452440.2235457092
1.8843-1.90910.25692620.2074447390
1.9091-1.93520.22612250.1911460892
1.9352-1.96290.22522100.1838451290
1.9629-1.99220.24882210.1808449089
1.9922-2.02330.22692060.178442389
2.0233-2.05650.21772060.174411181
2.0565-2.09190.22392560.175450092
2.0919-2.130.21562430.179464293
2.13-2.1710.23092400.1799469894
2.171-2.21530.2252660.1784460992
2.2153-2.26340.20332780.1723459393
2.2634-2.31610.20552430.1665454492
2.3161-2.3740.21022250.17461192
2.374-2.43820.21372670.1766444689
2.4382-2.50990.21542470.1807415784
2.5099-2.59090.20092410.1748470794
2.5909-2.68350.20362790.1703472195
2.6835-2.79090.18482200.1713469994
2.7909-2.91790.21462550.1781465193
2.9179-3.07170.21772510.1872458092
3.0717-3.26410.20132320.1734427486
3.2641-3.5160.19762280.1731481296
3.516-3.86970.17192430.1582479196
3.8697-4.42920.15912190.1387467493
4.4292-5.57840.17772120.1499459092
5.5784-43.5170.17372550.1549467894

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