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- PDB-1ym5: Crystal structure of YHI9, the yeast member of the phenazine bios... -

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Basic information

Entry
Database: PDB / ID: 1ym5
TitleCrystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
ComponentsHypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region
KeywordsOXIDOREDUCTASE / PhzF enzyme superfamily / double hot-dog / Structural Genomics / Paris-Sud Yeast Structural Genomics / YSG
Function / homology
Function and homology information


Isomerases; Racemases and epimerases / biosynthetic process / isomerase activity / endoplasmic reticulum unfolded protein response / chromatin / cytoplasm
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized isomerase YHI9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 Å
AuthorsLiger, D. / Quevillon-Cheruel, S. / Sorel, I. / Bremang, M. / Blondeau, K. / Aboulfath, I. / Janin, J. / Van Tilbeurgh, H. / Leulliot, N. / Paris-Sud Yeast Structural Genomics (YSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily
Authors: Liger, D. / Quevillon-Cheruel, S. / Sorel, I. / Bremang, M. / Blondeau, K. / Aboulfath, I. / Janin, J. / van Tilbeurgh, H. / Leulliot, N.
History
DepositionJan 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region


Theoretical massNumber of molelcules
Total (without water)33,4271
Polymers33,4271
Non-polymers00
Water2,774154
1
A: Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region

A: Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region


Theoretical massNumber of molelcules
Total (without water)66,8542
Polymers66,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)81.188, 81.188, 98.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region / YHI9


Mass: 33427.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pet9 / Production host: Escherichia coli (E. coli) / References: UniProt: P38765
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 24% PEG 4000, 0.1M sodium acetate pH5, 0.2M ammonium acetate, 30% glycerol, 10mM DDT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 2003
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.04→62.5 Å / Num. all: 21203 / Num. obs: 21044 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.043→2.096 Å / % possible all: 92.69

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.067 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0.4 / ESU R: 0.193 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25112 1081 5.1 %RANDOM
Rwork0.18763 ---
all0.1908 21044 --
obs0.1908 19923 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.236 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2--1.13 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 0 154 2446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222343
X-RAY DIFFRACTIONr_bond_other_d0.0010.022124
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9643177
X-RAY DIFFRACTIONr_angle_other_deg0.84634979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74525.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10415408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.387156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
X-RAY DIFFRACTIONr_nbd_refined0.2070.2470
X-RAY DIFFRACTIONr_nbd_other0.1890.22145
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21138
X-RAY DIFFRACTIONr_nbtor_other0.0920.21412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4241.51873
X-RAY DIFFRACTIONr_mcbond_other0.2361.5590
X-RAY DIFFRACTIONr_mcangle_it1.66422384
X-RAY DIFFRACTIONr_scbond_it2.39931017
X-RAY DIFFRACTIONr_scangle_it3.3084.5793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.043→2.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 80 -
Rwork0.261 1340 -
obs--92.69 %

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