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- PDB-2h4o: X-ray Crystal Structure of Protein yonK from Bacillus subtilis. N... -

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Basic information

Entry
Database: PDB / ID: 2h4o
TitleX-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415
ComponentsYonK protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Bsu2107 (YonK protein)
Function / homologyOB fold (Dihydrolipoamide Acetyltransferase, E2P) - #10 / Bacillus phage SPbeta, YonK / YonK superfamily / YonK protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Other non-globular / Special / SPbeta prophage-derived uncharacterized protein YonK
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSeetharaman, J. / Sue, M. / Forouhar, F. / Ken, C. / Bonnie, C. / Ma, L. / Xiao, R. / Acton, T.B. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the hypothetical protein from bacillus subtilis (yonk).
Authors: Seetharaman, J. / Sue, M. / Forouhar, F. / Ken, C. / Bonnie, C. / Ma, L. / Xiao, R. / Acton, T.B. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionMay 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YonK protein
B: YonK protein
C: YonK protein
D: YonK protein


Theoretical massNumber of molelcules
Total (without water)36,0504
Polymers36,0504
Non-polymers00
Water50428
1
A: YonK protein
B: YonK protein
C: YonK protein
D: YonK protein

A: YonK protein
B: YonK protein
C: YonK protein
D: YonK protein


Theoretical massNumber of molelcules
Total (without water)72,1008
Polymers72,1008
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area27180 Å2
ΔGint-136 kcal/mol
Surface area25690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.016, 72.201, 48.935
Angle α, β, γ (deg.)90.00, 113.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
YonK protein


Mass: 9012.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yonK / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: O31947
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 1000, 100mM TAPS pH 9.0, 120mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97913, 0.97941, 0.96780
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2005 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979131
20.979411
30.96781
ReflectionResolution: 2.8→50 Å / Num. all: 15558 / Num. obs: 15092 / % possible obs: 0.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: -0.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.046 / Net I/σ(I): 17.7
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 16.1 / Num. unique all: 1704 / Rsym value: 0.181 / % possible all: 0.99

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→28.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 868587.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1305 9.5 %RANDOM
Rwork0.263 ---
obs0.263 13805 88.6 %-
all-15120 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8049 Å2 / ksol: 0.320902 e/Å3
Displacement parametersBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.61 Å20 Å2-4.78 Å2
2---11.21 Å20 Å2
3---1.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 0 28 2032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 188 10.6 %
Rwork0.38 1578 -
obs-1704 68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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