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- PDB-2nyg: Crystal structure of YokD protein from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2nyg
TitleCrystal structure of YokD protein from Bacillus subtilis
ComponentsYokD protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / pfam02522 / NYSGXRC / 10116c / Aminoglycoside 3-N-acetyltransferase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / COENZYME A / SPbeta prophage-derived aminoglycoside N(3')-acetyltransferase-like protein YokD
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMadegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of YokD protein from Bacillus subtilis
Authors: Madegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN Atoms missing from COA were not modeled due to lack of electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YokD protein
B: YokD protein
C: YokD protein
D: YokD protein
E: YokD protein
F: YokD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,97211
Polymers186,1346
Non-polymers3,8385
Water4,017223
1
A: YokD protein
B: YokD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5804
Polymers62,0452
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-11 kcal/mol
Surface area22140 Å2
MethodPISA
2
C: YokD protein
D: YokD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5804
Polymers62,0452
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-20 kcal/mol
Surface area22540 Å2
MethodPISA
3
E: YokD protein
F: YokD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8123
Polymers62,0452
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-11 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.020, 132.390, 185.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
YokD protein


Mass: 31022.342 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yokD / Plasmid: pSGX4(BS) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: O32003
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M Lithium sulphate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12C10.9802
SYNCHROTRONNSLS X12C21.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDAug 14, 2006mirrors
ADSC QUANTUM 2102CCDAug 10, 2006mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.98021
21.11
ReflectionResolution: 2.37→50 Å / Num. all: 72328 / Num. obs: 72328 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.6
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.49 / Num. unique all: 6130 / % possible all: 82.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→49.04 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2587132.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to poor or lack of electron density. Residues with missing atoms listed in Remark 470 were modeled as ALA because of poor electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1145 2 %RANDOM
Rwork0.257 ---
obs0.257 56032 99.6 %-
all-56032 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.2461 Å2 / ksol: 0.335694 e/Å3
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.8 Å20 Å20 Å2
2---12.78 Å20 Å2
3---0.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12101 0 210 223 12534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 192 2.1 %
Rwork0.363 8866 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5coa-param.txtcoa-top.txt

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