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- PDB-1ng6: Structure of Cytosolic Protein of Unknown Function YqeY from Baci... -

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Basic information

Entry
Database: PDB / ID: 1ng6
TitleStructure of Cytosolic Protein of Unknown Function YqeY from Bacillus subtilis
ComponentsHypothetical protein yqeY
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Domain GatB/Yqey / pfam02637 / DUF186 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


carbon-nitrogen ligase activity, with glutamine as amido-N-donor
Similarity search - Function
Uncharacterised protein YqeY/AIM41, N-terminal domain / Arc Repressor Mutant, subunit A - #410 / Uncharacterised protein YqeY/Aim41 / YqeY/Aim41, N-terminal domain / Yqey-like protein / Hypothetical Protein Yqey; Chain: A; domain1 / Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 2 / Aspartyl/glutamyl-tRNA amidotransferase subunit B-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein YqeY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsZhang, R. / Dementiva, I. / Vinokour, E. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.4A crystal structure of hypothetical cytosolic protein YQEY
Authors: Zhang, R. / Dementiva, I. / Vinokour, E. / Collart, F. / Joachimiak, A.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _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

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Assembly

Deposited unit
A: Hypothetical protein yqeY


Theoretical massNumber of molelcules
Total (without water)16,7911
Polymers16,7911
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.463, 45.820, 44.361
Angle α, β, γ (deg.)90.00, 101.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein (APC1524) existed as monomer. One molecule in asymmetric unit.

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Components

#1: Protein Hypothetical protein yqeY


Mass: 16791.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YQEY / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P54464
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19%PEG3350, 5% PEG400, 0.1M Bis Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Dec 15, 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: 1.4→50 Å / Num. all: 27607 / Num. obs: 27414 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.95 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 30
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2661 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→34.71 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections for refinement is greater than the number of reflections for data collection because in cns refinement (hlml target), the Fridel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2538 4.9 %RANDOM
Rwork0.21 ---
obs0.21 51310 95 %-
all-54010 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5572 Å2 / ksol: 0.336155 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å21.34 Å2
2--0.63 Å20 Å2
3---0.19 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.4→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 295 1464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.1
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 371 4.8 %
Rwork0.298 7336 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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