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- PDB-3onq: Crystal Structure of Regulator of Polyketide Synthase Expression ... -

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Basic information

Entry
Database: PDB / ID: 3onq
TitleCrystal Structure of Regulator of Polyketide Synthase Expression BAD_0249 from Bifidobacterium adolescentis
ComponentsRegulator of polyketide synthase expression
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / helix-bundle / alpha-beta-alpha sandwich / Signal transduction / cytosol
Function / homology
Function and homology information


PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5100 / Alpha-Beta Plaits - #2730 / PucR C-terminal helix-turn-helix domain / PucR C-terminal helix-turn-helix domain superfamily / PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Up-down Bundle ...PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5100 / Alpha-Beta Plaits - #2730 / PucR C-terminal helix-turn-helix domain / PucR C-terminal helix-turn-helix domain superfamily / PucR C-terminal helix-turn-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HTH_30 domain-containing protein
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.098 Å
AuthorsKim, Y. / Wu, R. / Tan, K. / Morales, J. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Regulator of Polyketide Synthase Expression BAD_0249 from Bifidobacterium adolescentis
Authors: Kim, Y. / Wu, R. / Tan, K. / Morales, J. / Bearden, J. / Joachimiak, A.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of polyketide synthase expression
B: Regulator of polyketide synthase expression
C: Regulator of polyketide synthase expression
D: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,00139
Polymers115,6864
Non-polymers3,31535
Water14,142785
1
A: Regulator of polyketide synthase expression
C: Regulator of polyketide synthase expression
hetero molecules

B: Regulator of polyketide synthase expression
D: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,00139
Polymers115,6864
Non-polymers3,31535
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area13070 Å2
ΔGint-325 kcal/mol
Surface area43370 Å2
MethodPISA
2
A: Regulator of polyketide synthase expression
C: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,73622
Polymers57,8432
Non-polymers1,89320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-170 kcal/mol
Surface area23140 Å2
MethodPISA
3
B: Regulator of polyketide synthase expression
D: Regulator of polyketide synthase expression
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,26417
Polymers57,8432
Non-polymers1,42115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-135 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.452, 93.452, 166.687
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
Regulator of polyketide synthase expression


Mass: 28921.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (bacteria)
Strain: ATCC 15703 / Gene: BAD_0249 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: A0ZZZ7
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris-Propane:NaOH pH 7.0, 1.5 M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 22, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 78815 / Num. obs: 78815 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 31.69 Å2 / Rsym value: 0.105 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4 / Num. unique all: 3908 / Rsym value: 0.725 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.098→39.811 Å / SU ML: 0.3 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3901 5.05 %random
Rwork0.173 ---
all0.175 77313 --
obs0.175 77313 98.16 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.213 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.5917 Å20 Å20 Å2
2--3.7708 Å2-0 Å2
3---0.8209 Å2
Refinement stepCycle: LAST / Resolution: 2.098→39.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 187 785 8589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087974
X-RAY DIFFRACTIONf_angle_d1.03610867
X-RAY DIFFRACTIONf_dihedral_angle_d13.1872892
X-RAY DIFFRACTIONf_chiral_restr0.0721247
X-RAY DIFFRACTIONf_plane_restr0.0061399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0983-2.17320.25943820.20417210759298
2.1732-2.26020.26513800.21437177755797
2.2602-2.36310.25773870.21167090747796
2.3631-2.48770.25083760.19567215759197
2.4877-2.64350.22523510.19667280763197
2.6435-2.84760.24313910.19267281767298
2.8476-3.1340.22834020.18737366776899
3.134-3.58730.19844010.177674667867100
3.5873-4.51860.16023980.137475327930100
4.5186-39.81790.16944330.157977958228100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2740.10760.00360.7442-0.83111.50150.08150.0273-0.1606-0.16980.08950.10560.2863-0.1519-0.16150.2336-0.0443-0.04860.18160.04480.249147.8729.783559.5799
21.0334-0.49560.16480.3346-0.01390.6783-0.03290.1541-0.0854-0.0031-0.01750.0298-0.0166-0.07960.04990.1297-0.01330.01670.1742-0.02470.1361.126714.070520.8336
30.62510.13610.02530.626-0.10380.46960.049-0.0704-0.08070.02-0.0481-0.0124-0.0288-0.014-0.00390.16440.00110.00310.18530.03550.184466.295647.803572.4027
40.69070.3007-0.81810.7996-0.34841.2525-0.0357-0.2316-0.03050.0637-0.011-0.00540.08620.34490.04350.210.0128-0.02090.27860.0170.204770.53966.034346.2661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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