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- PDB-3ed5: The crystal structure of YfnB from Bacillus subtilis subsp. subti... -

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Basic information

Entry
Database: PDB / ID: 3ed5
TitleThe crystal structure of YfnB from Bacillus subtilis subsp. subtilis str. 168
ComponentsYfnB
Keywordsstructural genomics / unknown function / APC60080 / YfnB / Bacillus subtilis subsp. subtilis str. 168 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Hydrolases / 5'-nucleotidase activity
Similarity search - Function
HAD-superfamily hydrolase, subfamily IA, YjjG/PynA / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...HAD-superfamily hydrolase, subfamily IA, YjjG/PynA / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Putative HAD-hydrolase YfnB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsTan, K. / Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of YfnB from Bacillus subtilis subsp. subtilis str. 168
Authors: Tan, K. / Wu, R. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YfnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,42411
Polymers27,9641
Non-polymers46010
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.186, 91.186, 68.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsAuthors state that the biological unit is experimentally unknown. It is predicted to be a monomer.

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Components

#1: Protein YfnB


Mass: 27963.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: str. 168 / Gene: yfnB, BSU07330 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O06480
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.5M Sodium Format 0.1M Sodium Acetate Trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97948 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 8, 2008 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.72→26 Å / Num. all: 34185 / Num. obs: 34185 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 32.2
Reflection shellResolution: 1.72→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.82 / Num. unique all: 1337 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→25.82 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.145 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19725 1729 5.1 %RANDOM
Rwork0.17113 ---
all0.17245 32418 --
obs0.17245 32418 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.72→25.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 30 191 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9692744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78124.685111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7671513
X-RAY DIFFRACTIONr_chiral_restr0.10.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.51201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4721917
X-RAY DIFFRACTIONr_scbond_it2.4963833
X-RAY DIFFRACTIONr_scangle_it4.0624.5818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.721→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 124 -
Rwork0.318 2348 -
obs-2472 99.6 %
Refinement TLS params.Method: refined / Origin x: 2.597 Å / Origin y: 35.055 Å / Origin z: 1.247 Å
111213212223313233
T-0.1582 Å20.0028 Å20.0341 Å2--0.1491 Å20.0137 Å2---0.2087 Å2
L0.9365 °20.0794 °20.3052 °2-1.1469 °20.5301 °2--1.1851 °2
S-0.0497 Å °0.0117 Å °-0.0791 Å °0.0206 Å °0.0977 Å °0.0234 Å °-0.0528 Å °0.0239 Å °-0.0481 Å °

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