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- PDB-3r2q: Crystal Structure Analysis of yibF from E. Coli -

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Basic information

Entry
Database: PDB / ID: 3r2q
TitleCrystal Structure Analysis of yibF from E. Coli
ComponentsUncharacterized GST-like protein yibF
KeywordsTRANSFERASE / glutathione / GST
Function / homology
Function and homology information


maleylacetoacetate isomerase activity / L-phenylalanine catabolic process / glutathione transferase activity / glutathione metabolic process / cytosol
Similarity search - Function
Uncharacterized GST-like protein YibF / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Uncharacterized GST-like protein YibF / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / PHOSPHATE ION / Uncharacterized GST-like protein YibF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
AuthorsLadner, J.E. / Harp, J. / Schaab, M. / Stournan, N.V. / Armstrong, R.N.
CitationJournal: to be published
Title: Structural and Functional Genomics of YibF, a Glutathione Transferase Homologue from Escherichia coli
Authors: Ladner, J.E. / Stournan, N.V. / Branch, M.C. / Harp, J. / Schaab, M. / Brown, D.W. / Armstrong, R.N.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized GST-like protein yibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1115
Polymers22,5851
Non-polymers5264
Water5,062281
1
A: Uncharacterized GST-like protein yibF
hetero molecules

A: Uncharacterized GST-like protein yibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,22310
Polymers45,1702
Non-polymers1,0538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_455-x-3/4,-z+1/4,-y+1/41
Buried area6110 Å2
ΔGint-28 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.340, 111.340, 111.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-1089-

HOH

21A-1186-

HOH

31A-1243-

HOH

41A-1248-

HOH

51A-1251-

HOH

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Components

#1: Protein Uncharacterized GST-like protein yibF


Mass: 22585.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3592, JW3565, yibF / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACA1
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 5 microL protein in 50 mM HEPES pH 7.5, 1 mM DTT, 4 microL reservoir (0.1M Na acetate pH 4.6,1M ammonium phosphate monobasic), 1 microL 100mM glutathione pH 7.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 107437 / % possible obs: 98.1 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.2
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.465 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å9.96 Å
Translation3 Å9.96 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER1.3.3phasing
SHELXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
ARP/wARPmodel building
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.05→26 Å / Num. parameters: 18731 / Num. restraintsaints: 25172 / Redundancy reflection obs: 102007 / Occupancy max: 1 / Occupancy min: 0.11 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT, FINAL REFINEMENT WITH RIDING HYDROGENS
RfactorNum. reflection% reflectionSelection details
Rfree0.1528 5366 5 %RANDOM
all0.1317 ---
obs-107373 93.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 16.7281 Å2
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 1584 / Occupancy sum non hydrogen: 1876.55
Refinement stepCycle: LAST / Resolution: 1.05→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 33 281 1901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0268
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.213
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.099

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