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- PDB-3oms: Putative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein... -

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Basic information

Entry
Database: PDB / ID: 3oms
TitlePutative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein, from Bacillus cereus.
ComponentsPhnB protein
KeywordsTRANSFERASE / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / methyltransferase / glyoxalase family
Function / homology
Function and homology information


Signal recognition particle alu RNA binding heterodimer, srp9/1 - #100 / Predicted 3-demethylubiquinone-9 3-methyltransferase, bacterial / Predicted 3-demethylubiquinone-9 3-methyltransferase / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #110 / PhnB-like / 3-demethylubiquinone-9 3-methyltransferase / Signal recognition particle alu RNA binding heterodimer, srp9/1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Li, H. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative 3-demethylubiquinone-9 3-methyltransferase, PhnB protein, from Bacillus cereus.
Authors: Osipiuk, J. / Li, H. / Abdullah, J. / Joachimiak, A.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 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: PhnB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0023
Polymers15,8781
Non-polymers1242
Water1,856103
1
A: PhnB protein
hetero molecules

A: PhnB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0046
Polymers31,7562
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3520 Å2
ΔGint-14 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.302, 62.302, 90.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PhnB protein


Mass: 15877.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_2431 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81DD6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 40% PEG-300, 0.1 M phoshate citrate buffer, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 11, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→36.7 Å / Num. all: 14643 / Num. obs: 14643 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.138 / Χ2: 3.39 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.9317.40.8563.097150.762100
1.93-1.9717.30.717080.771100
1.97-2.0117.30.5087240.759100
2.01-2.0517.40.4047000.847100
2.05-2.0917.20.3497130.996100
2.09-2.1417.30.3117280.923100
2.14-2.1917.20.2957021.085100
2.19-2.2517.10.2737351.286100
2.25-2.3217.10.2457161.435100
2.32-2.39170.2217261.538100
2.39-2.48170.2227231.911100
2.48-2.5816.70.1957182.368100
2.58-2.716.50.187303.114100
2.7-2.8416.20.1697373.919100
2.84-3.0215.80.1537304.903100
3.02-3.2514.90.1287466.084100
3.25-3.5814.10.1167347.403100
3.58-4.0912.70.1057618.85399.9
4.09-5.1610.20.09976911.15599.6
5.16-5011.60.11582816.18797.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→36.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.132 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 727 5 %RANDOM
Rwork0.1798 ---
all0.1814 14535 --
obs0.1814 14535 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.23 Å2 / Biso mean: 37.193 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 8 103 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221117
X-RAY DIFFRACTIONr_bond_other_d0.0030.02736
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9331522
X-RAY DIFFRACTIONr_angle_other_deg0.931810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20425.35756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.823151
X-RAY DIFFRACTIONr_chiral_restr0.0890.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_mcbond_it0.9611.5663
X-RAY DIFFRACTIONr_mcbond_other0.2761.5270
X-RAY DIFFRACTIONr_mcangle_it1.70621080
X-RAY DIFFRACTIONr_scbond_it2.5193454
X-RAY DIFFRACTIONr_scangle_it4.0814.5434
LS refinement shellResolution: 1.902→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 60 -
Rwork0.254 990 -
all-1050 -
obs-1054 99.34 %
Refinement TLS params.Method: refined / Origin x: 5.6391 Å / Origin y: 11.5424 Å / Origin z: 36.6645 Å
111213212223313233
T0.0585 Å2-0.051 Å2-0.044 Å2-0.062 Å20.0319 Å2--0.0553 Å2
L3.1842 °2-0.3238 °2-0.3797 °2-1.5083 °2-0.213 °2--2.3468 °2
S-0.0614 Å °0.1872 Å °0.0293 Å °-0.0728 Å °0.0171 Å °-0.0668 Å °-0.0096 Å °-0.1116 Å °0.0443 Å °

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