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- PDB-1mk4: Structure of Protein of Unknown Function YqjY from Bacillus subti... -

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Basic information

Entry
Database: PDB / ID: 1mk4
TitleStructure of Protein of Unknown Function YqjY from Bacillus subtilis, Probable Acetyltransferase
ComponentsHypothetical protein yqjY
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase, GNAT, predicted / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YqjY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsZhang, R. / Dementiva, I. / Mo, A. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.7A crystal structure of a hypothetical protein yqjY from Bacillus subtilis
Authors: Zhang, R. / Dementiva, I. / Mo, A. / Collart, F. / Joachimiak, A.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 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 ...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 protein yqjY
B: Hypothetical protein yqjY


Theoretical massNumber of molelcules
Total (without water)36,0272
Polymers36,0272
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-3 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.613, 103.613, 72.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThis protein existed as dimer(MolA and MolB)

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Components

#1: Protein Hypothetical protein yqjY


Mass: 18013.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YQJY / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: P54562
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, 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: Jul 31, 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: 1.7→28.09 Å / Num. all: 48445 / Num. obs: 48073 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.14 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 27
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.59 / Num. unique all: 53174 / % possible all: 98.6

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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 / Resolution: 1.7→28.09 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: Freidel pairs were used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4491 4.9 %RANDOM
Rwork0.22 ---
all-95267 --
obs-91171 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.4471 Å2 / ksol: 0.363244 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å21.08 Å20 Å2
2--0.94 Å20 Å2
3----1.89 Å2
Refine analyzeLuzzati coordinate error free: 0.23 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 0 325 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it0.71.5
X-RAY DIFFRACTIONc_mcangle_it1.272
X-RAY DIFFRACTIONc_scbond_it12
X-RAY DIFFRACTIONc_scangle_it1.542.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 692 4.9 %
Rwork0.261 13381 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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