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- PDB-1xaf: Crystal Structure of Protein of Unknown Function YfiH from Shigel... -

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Basic information

Entry
Database: PDB / ID: 1xaf
TitleCrystal Structure of Protein of Unknown Function YfiH from Shigella flexneri 2a str. 2457T
Componentsorf, conserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / MCSG / Hypothetical protein / YfiH / Shigella flexneri 2a str. 2457T / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


2'-deoxyadenosine deaminase activity / adenosine deaminase / S-methyl-5'-thioadenosine phosphorylase / adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / purine-nucleoside phosphorylase / oxidoreductase activity / copper ion binding
Similarity search - Function
CNF1/YfiH-like putative cysteine hydrolases / CNF1/YfiH-like putative cysteine hydrolases / Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Purine nucleoside phosphorylase YfiH / Purine nucleoside phosphorylase YfiH
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsKim, Y. / Maltseva, N. / Dementieva, I. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 A resolution.
Authors: Kim, Y. / Maltseva, N. / Dementieva, I. / Collart, F. / Holzle, D. / Joachimiak, A.
History
DepositionAug 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: orf, conserved hypothetical protein
B: orf, conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,64917
Polymers53,6462
Non-polymers1,00315
Water7,566420
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.874, 50.583, 55.347
Angle α, β, γ (deg.)90.32, 96.32, 90.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein orf, conserved hypothetical protein


Mass: 26823.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Species: Shigella flexneri / Strain: 2457T / Gene: YfiH / Plasmid details: T7 promoter / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q83K13, UniProt: A0A384KG77*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.2 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 17, 2004 / Details: mirrors
RadiationMonochromator: Double crystal SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.01→55.05 Å / Num. all: 31355 / Num. obs: 30856 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.3
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6.5 / Num. unique all: 2849 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→55.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.636 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25159 3071 10 %RANDOM
Rwork0.1786 ---
all0.18583 27582 --
obs0.18583 27582 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0.07 Å2-0.81 Å2
2---0.79 Å20.03 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.01→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 40 420 4148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9575163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40923.293164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6515585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4851528
X-RAY DIFFRACTIONr_chiral_restr0.1030.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022944
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21914
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2418
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0611.52479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50523850
X-RAY DIFFRACTIONr_scbond_it2.61731523
X-RAY DIFFRACTIONr_scangle_it3.6194.51313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.007→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.282 188
Rwork0.209 1813
obs-1813

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