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- PDB-3ho7: Crystal structure of OxyR from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 3ho7
TitleCrystal structure of OxyR from Porphyromonas gingivalis
ComponentsOxyR
KeywordsTRANSCRIPTION / beta-alpha-barrels / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Redox-sensitive transcriptional activator OxyR
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.58 Å
AuthorsSvintradze, D.V. / Wright, H.T. / Lewis, J.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis.
Authors: Svintradze, D.V. / Peterson, D.L. / Collazo-Santiago, E.A. / Lewis, J.P. / Wright, H.T.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 16, 2013Group: Atomic model
Revision 1.3Oct 2, 2013Group: Database references
Revision 1.4Jan 8, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OxyR
B: OxyR


Theoretical massNumber of molelcules
Total (without water)53,3832
Polymers53,3832
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-11 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.819, 55.795, 56.711
Angle α, β, γ (deg.)110.63, 102.82, 114.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
/ NCS domain segments: (Refine code: 1 )

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Components

#1: Protein OxyR / Redox-sensitive transcriptional activator OxyR


Mass: 26691.725 Da / Num. of mol.: 2 / Fragment: REGULATORY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: ATCC 33277 / DSM 20709 / JCM 12257 / Gene: oxyR, PG_0270 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MXD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5451.51
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
291.151vapor diffusion, hanging drop7.512% PEG 8K, 8% EG, 0.1M HEPES BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
291.152vapor diffusion, sitting drop7.512% PEG 8K, 8% EG, 0.1M HEPES BUFFER, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
3931
1,2,31
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.5418
ROTATING ANODERIGAKU MICROMAX-00721.5418
ROTATING ANODERIGAKU MICROMAX-00731.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEFeb 4, 2009MSC Varimax confocal optics
RIGAKU RAXIS IV++2IMAGE PLATEMar 19, 2009MSC Varimax confocal optics
RIGAKU RAXIS IV++3IMAGE PLATEMar 27, 2009MSC Varimax confocal optics
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1copperSINGLE WAVELENGTHMx-ray1
2copperSINGLE WAVELENGTHMx-ray1
3copperSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.513
11K, H, -H-K-L20.487
ReflectionResolution: 1.58→26.94 Å / Num. all: 127008 / Num. obs: 59646 / % possible obs: 86.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3.7 / Redundancy: 3.92 % / Rmerge(I) obs: 0.032
Reflection shellHighest resolution: 1.58 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.032 / % possible all: 86.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
REFMAC5.5.0066refinement
d*TREKdata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.58→26.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.295 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24456 2033 3.4 %RANDOM
Rwork0.2194 ---
obs0.22028 57380 83.56 %-
all-59646 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.429 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.59 Å2-6.77 Å2
2--1.22 Å25.57 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.58→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 0 418 3952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223608
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6481.984876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2835438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56222.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36715658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5661538
X-RAY DIFFRACTIONr_chiral_restr0.0430.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212714
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_it0.211.52194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38523548
X-RAY DIFFRACTIONr_scbond_it0.53831414
X-RAY DIFFRACTIONr_scangle_it0.8564.51328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
560medium positional0.170.5
562loose positional0.365
560medium thermal1.092
562loose thermal1.1410
LS refinement shellResolution: 1.581→1.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 37 -
Rwork0.284 1164 -
obs--22.76 %
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)
10.3840.02080.71541.73690.48912.19810.05260.0074-0.0457-0.07480.00390.07190.03690.1889-0.05660.0162-0.0085-0.00090.0526-0.00760.0355-9.49721.38218.314
21.5430.32020.05170.7765-0.57031.87430.0298-0.0658-0.10590.00780.0280.049-0.114-0.12-0.05780.03890.01420.0120.0150.00660.0376-29.95234.08425.99
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A90 - 309
2X-RAY DIFFRACTION1A2 - 80
3X-RAY DIFFRACTION1A313 - 519
4X-RAY DIFFRACTION2B90 - 309
5X-RAY DIFFRACTION2B1 - 78
6X-RAY DIFFRACTION2B313 - 518

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