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- PDB-3gve: Crystal structure of calcineurin-like phosphoesterase YfkN from B... -

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Basic information

Entry
Database: PDB / ID: 3gve
TitleCrystal structure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis
ComponentsYfkN protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta-beta-alpha sandwich / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Metal-binding / Nucleotide-binding
Function / homology
Function and homology information


2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / 3'-nucleotidase / 3'-nucleotidase activity / nucleotide catabolic process / 5'-nucleotidase / 5'-nucleotidase activity / cell wall / outer membrane-bounded periplasmic space / nucleotide binding ...2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / 3'-nucleotidase / 3'-nucleotidase activity / nucleotide catabolic process / 5'-nucleotidase / 5'-nucleotidase activity / cell wall / outer membrane-bounded periplasmic space / nucleotide binding / extracellular region / metal ion binding
Similarity search - Function
CpdB, N-terminal metallophosphatase domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...CpdB, N-terminal metallophosphatase domain / 5'-nucleotidase signature 1. / 5'-Nucleotidase, conserved site / 5'-nucleotidase signature 2. / 5'-Nucleotidase, C-terminal / 5'-nucleotidase, C-terminal domain / 5'-Nucleotidase/apyrase / 5'-Nucleotidase, C-terminal domain superfamily / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / : / Trifunctional nucleotide phosphoesterase protein YfkN
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsKim, Y. / Marshall, N. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Calcineurin-like Phosphoesterase from Bacillus subtilis
Authors: Kim, Y. / Marshall, N. / Cobb, G. / Joachimiak, A.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YfkN protein
B: YfkN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5239
Polymers74,9562
Non-polymers5677
Water14,646813
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.091, 92.505, 50.316
Angle α, β, γ (deg.)90.00, 89.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YfkN protein


Mass: 37477.809 Da / Num. of mol.: 2 / Fragment: UNP residues 37-374
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag with TEV protease cut-site
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU07840, yfkN / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: O34313
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.4 M Sodium citrate tribasic dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.25→31.536 Å / Num. all: 169020 / Num. obs: 169020 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 11.53 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.5
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4231 / % possible all: 98.7

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Processing

Software
NameClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.25→31.536 Å / SU ML: 0.12 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.163 8483 5.02 %random
Rwork0.154 ---
all0.154 169020 --
obs0.154 169020 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.82 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2414 Å2-0 Å2-0.214 Å2
2---0.902 Å20 Å2
3----0.3394 Å2
Refinement stepCycle: LAST / Resolution: 1.25→31.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5146 0 31 813 5990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.018
X-RAY DIFFRACTIONf_angle_d1.508
X-RAY DIFFRACTIONf_dihedral_angle_deg19.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.25-1.26170.26672250.23124551477684
1.2617-1.27650.22632700.2096530899
1.2765-1.29210.20082920.1935421100
1.2921-1.30840.22882800.18655294100
1.3084-1.32560.22462690.17815398100
1.3256-1.34380.19292630.17115411100
1.3438-1.3630.18282770.15455408100
1.363-1.38330.17032710.15175324100
1.3833-1.4050.17842780.14755432100
1.405-1.4280.17042660.1435361100
1.428-1.45260.16693180.14345346100
1.4526-1.4790.15852670.13685395100
1.479-1.50750.1582850.13025355100
1.5075-1.53820.15982850.12435400100
1.5382-1.57170.14342810.12645393100
1.5717-1.60830.1532760.12635372100
1.6083-1.64850.14512890.12675370100
1.6485-1.6930.15622930.13175341100
1.693-1.74290.15783120.13685382100
1.7429-1.79910.14722970.14235356100
1.7991-1.86340.15892880.14325439100
1.8634-1.9380.15222890.14135351100
1.938-2.02620.15833080.14035346100
2.0262-2.1330.14762810.13685384100
2.133-2.26660.14213030.13855392100
2.2666-2.44150.1492870.15175394100
2.4415-2.68710.16592940.16155406100
2.6871-3.07570.17572640.16665431100
3.0757-3.87390.13782790.14555437100
3.8739-31.5460.1532960.1501533997

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