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- PDB-3kwo: Crystal Structure of Putative Bacterioferritin from Campylobacter... -

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Basic information

Entry
Database: PDB / ID: 3kwo
TitleCrystal Structure of Putative Bacterioferritin from Campylobacter jejuni
ComponentsPutative bacterioferritin
KeywordsOXIDOREDUCTASE / alpha-helix / bacterial ferritin fold / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Cytoplasm / Iron / Iron storage / Metal-binding
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / DNA protection / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm
Similarity search - Function
DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / 1,4-BUTANEDIOL / DNA protection during starvation protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.985 Å
AuthorsKim, Y. / Gu, M. / Papazisi, L. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Bacterioferritin from Campylobacter jejuni
Authors: Kim, Y. / Gu, M. / Papazisi, L. / Anderson, W. / Joachimiak, A.
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 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: Putative bacterioferritin
B: Putative bacterioferritin
C: Putative bacterioferritin
D: Putative bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,71859
Polymers71,1224
Non-polymers3,59655
Water10,323573
1
A: Putative bacterioferritin
B: Putative bacterioferritin
C: Putative bacterioferritin
D: Putative bacterioferritin
hetero molecules

A: Putative bacterioferritin
B: Putative bacterioferritin
C: Putative bacterioferritin
D: Putative bacterioferritin
hetero molecules

A: Putative bacterioferritin
B: Putative bacterioferritin
C: Putative bacterioferritin
D: Putative bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,154177
Polymers213,36512
Non-polymers10,789165
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area48240 Å2
ΔGint-2846 kcal/mol
Surface area66340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.715, 91.715, 202.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11D-170-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative bacterioferritin /


Mass: 17780.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Species: subsp. jejuni NCTC 11168 / Strain: NCTC 11168 / Plasmid: Magic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0P891

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Non-polymers , 5 types, 628 molecules

#2: Chemical...
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Zinc acetate, 0.1 M Imidazole pH 8.0, 20% (v/v) 1,4-bdiolutaiediol, 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: 0.97934 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.98→28.78 Å / Num. all: 43678 / Num. obs: 43678 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.54
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.51 / Rsym value: 0.854 / % possible all: 76.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.985→28.78 Å / SU ML: 0.21 / Isotropic thermal model: mixed / σ(F): 1.96 / Phase error: 18.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1965 2172 5.03 %
Rwork0.1436 --
obs0.1462 43169 98.37 %
all-43169 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.044 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1165 Å20 Å2-0 Å2
2--3.1165 Å20 Å2
3----6.233 Å2
Refinement stepCycle: LAST / Resolution: 1.985→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 152 573 5550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135028
X-RAY DIFFRACTIONf_angle_d1.3756750
X-RAY DIFFRACTIONf_dihedral_angle_d16.9451801
X-RAY DIFFRACTIONf_chiral_restr0.091727
X-RAY DIFFRACTIONf_plane_restr0.006868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9845-2.05540.22952160.17563970X-RAY DIFFRACTION96
2.0554-2.13770.24232240.16634089X-RAY DIFFRACTION98
2.1377-2.2350.20642120.15044073X-RAY DIFFRACTION98
2.235-2.35270.21642290.14594047X-RAY DIFFRACTION98
2.3527-2.50010.21372190.14364119X-RAY DIFFRACTION98
2.5001-2.6930.20272190.13984096X-RAY DIFFRACTION99
2.693-2.96370.18932080.13554161X-RAY DIFFRACTION99
2.9637-3.3920.19262070.13844143X-RAY DIFFRACTION99
3.392-4.27130.15622010.12734172X-RAY DIFFRACTION100
4.2713-28.78280.19432370.14384127X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.7979-0.3674-0.25550.51030.17370.45560.01050.02160.0163-0.04010.0132-0.0032-0.0879-0.0077-0.02140.1078-0.01590.00110.05690.03050.041322.70963.9932170.2
20.52760.050.09890.2105-0.22630.71490.0216-0.00880.07690.0153-0.00120.0058-0.1173-0.0147-0.01410.1532-0.00020.0080.0747-0.02130.1137
30.4123-0.2688-0.04580.69780.01980.64730.03720.01660.0356-0.0433-0.0115-0.0274-0.07810.1269-0.02050.0836-0.04240.00960.10990.00750.0936
40.43180.0581-0.21050.41110.10450.4688-0.0026-0.0671-0.04070.0653-0.0089-0.03160.01370.07140.00230.0921-0.0037-0.03480.1089-0.00690.0745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-1 - 168
2X-RAY DIFFRACTION2chain BB1 - 167
3X-RAY DIFFRACTION3chain CC1 - 166
4X-RAY DIFFRACTION4chain DD0 - 166

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