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- PDB-1twu: 2.0 A Crystal Structure of a YycE Protein of Unknown Function fro... -

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Basic information

Entry
Database: PDB / ID: 1twu
Title2.0 A Crystal Structure of a YycE Protein of Unknown Function from Bacillus subtilis, Putative Glyoxalase/Fosfomycin Resistance Protein
ComponentsHypothetical protein yycE
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein structure initiative / MCSG / duplication of the alpha-beta sandwichs. Bacillus subtilis / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


YycE-like N-terminal domain / YycE-like C-terminal domain / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YycE
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Quartey, P. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.0 A crystal structure of a hypothetical protein yycE from Bacillus subtilis
Authors: Zhang, R. / Quartey, P. / Collart, F. / Joachimiak, A.
History
DepositionJul 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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

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Assembly

Deposited unit
A: Hypothetical protein yycE


Theoretical massNumber of molelcules
Total (without water)15,6051
Polymers15,6051
Non-polymers00
Water1,42379
1
A: Hypothetical protein yycE

A: Hypothetical protein yycE


Theoretical massNumber of molelcules
Total (without water)31,2092
Polymers31,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5000 Å2
ΔGint-31 kcal/mol
Surface area11940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.773, 59.773, 112.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThis protein exists as dimer.The second part of the biological assembly is generated by the two fold axis:-x,-y,-z

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Components

#1: Protein Hypothetical protein yycE


Mass: 15604.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: YYCE or BSU40430 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37479
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.215 Å3/Da / Density % sol: 60.27 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9795 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 18, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 26277 / Num. obs: 25357 / % possible obs: 96.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 5.2 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2631 / % possible all: 75.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→39.55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 269090.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1155 4.8 %RANDOM
Rwork0.207 ---
all0.212 26274 --
obs0.207 24172 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1179 Å2 / ksol: 0.361403 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.58 Å20 Å20 Å2
2--5.58 Å20 Å2
3----11.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 0 79 1168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 154 4.8 %
Rwork0.298 3080 -
obs-2615 73.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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