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- PDB-5eur: Hypothetical protein SF216 from shigella flexneri 5a M90T -

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Basic information

Entry
Database: PDB / ID: 5eur
TitleHypothetical protein SF216 from shigella flexneri 5a M90T
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Shigella flexneri / Structural genomics / Glutathione S-transferase / Putative hot spot
Function / homology:
Function and homology information
Biological speciesShigella flexneri 5a str. M90T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.698 Å
AuthorsLee, Y.-S. / Seok, S.-H. / Kim, H.-N. / An, J.-G. / Chung, K.Y. / Won, H.-S. / Seo, M.-D.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea2012R1A1A1039738 Korea, Republic Of
National Research Foundation of Korea2014R1A1A2054691 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of SF216 from Shigella flexneri strain 5a
Authors: Lee, Y.-S. / Seok, S.-H. / Kim, H.-N. / An, J.-G. / Chung, K.Y. / Won, H.-S. / Seo, M.-D.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8505
Polymers45,7303
Non-polymers1202
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-59 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.399, 50.411, 99.921
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-292-

HOH

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Components

#1: Protein Uncharacterized protein / SF216


Mass: 15243.169 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 5a str. M90T (bacteria)
Gene: SF5M90T_216 / Plasmid: pET21a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: A0A0F6M9P9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 47.31 %
Description: hexahedron in shape, with two trapezoidal faces
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium HEPES, 2 M ammonium sulfate, 2% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. obs: 44562 / % possible obs: 95.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 19.13 Å2 / Rmerge(I) obs: 0.013 / Net I/σ(I): 36.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 6.2 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PHENIXmodel building
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.698→24.478 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 2016 4.52 %
Rwork0.2046 --
obs0.2062 44556 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→24.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 6 279 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062694
X-RAY DIFFRACTIONf_angle_d0.9073612
X-RAY DIFFRACTIONf_dihedral_angle_d12.71637
X-RAY DIFFRACTIONf_chiral_restr0.053390
X-RAY DIFFRACTIONf_plane_restr0.004468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6975-1.740.23931220.21322858X-RAY DIFFRACTION89
1.74-1.7870.20571450.19663053X-RAY DIFFRACTION96
1.787-1.83960.22521380.1872960X-RAY DIFFRACTION95
1.8396-1.89890.19861500.17982996X-RAY DIFFRACTION94
1.8989-1.96680.23041350.19382963X-RAY DIFFRACTION93
1.9668-2.04550.23081420.19632956X-RAY DIFFRACTION93
2.0455-2.13850.24251490.18492955X-RAY DIFFRACTION93
2.1385-2.25120.22931400.18862977X-RAY DIFFRACTION94
2.2512-2.39210.2361440.2052997X-RAY DIFFRACTION93
2.3921-2.57660.21191400.20413066X-RAY DIFFRACTION96
2.5766-2.83560.21641490.20793128X-RAY DIFFRACTION98
2.8356-3.24510.24891540.20723180X-RAY DIFFRACTION100
3.2451-4.08540.25631510.19813218X-RAY DIFFRACTION100
4.0854-24.48040.26941570.23073233X-RAY DIFFRACTION98

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