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- PDB-1nc5: Structure of Protein of Unknown Function of YteR from Bacillus Su... -

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Basic information

Entry
Database: PDB / ID: 1nc5
TitleStructure of Protein of Unknown Function of YteR from Bacillus Subtilis
Componentshypothetical protein yTER
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HELIX BARREL / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


unsaturated rhamnogalacturonyl hydrolase / unsaturated rhamnogalacturonyl hydrolase activity / carbohydrate metabolic process / cytoplasm
Similarity search - Function
: / Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Unsaturated rhamnogalacturonyl hydrolase YteR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsZhang, R. / Lozondra, L. / Korolev, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2005
Title: 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase.
Authors: Zhang, R. / Minh, T. / Lezondra, L. / Korolev, S. / Moy, S.F. / Collart, F. / Joachimiak, A.
History
DepositionDec 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein yTER


Theoretical massNumber of molelcules
Total (without water)43,0221
Polymers43,0221
Non-polymers00
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.855, 91.855, 179.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThis protein (APC1644) existed as monomer

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Components

#1: Protein hypothetical protein yTER


Mass: 43021.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YTER / Plasmid: MSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: O34559
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3 M Nacitrate, 0.1M Tris , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
21.3 Msodium citrate1reservoir
30.1 MTris1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Nov 12, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 1.6→50 Å / Num. obs: 59605 / % possible obs: 99.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 20.36 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 34.88
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.47 / Num. unique all: 5741 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 59188
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.56

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 1.6→44.49 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: In the cns refinement (hlml target), the Friedel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 5231 4.9 %RANDOM
Rwork0.187 ---
obs0.187 106074 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3677 Å2 / ksol: 0.389443 e/Å3
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.65 Å20 Å2
2--1.23 Å20 Å2
3----2.46 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 0 499 3460
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it0.751.5
X-RAY DIFFRACTIONc_mcangle_it1.262
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_scangle_it2.182.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 767 4.9 %
Rwork0.266 15037 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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