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- PDB-3t22: Crystal structure of OxyR mutant from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 3t22
TitleCrystal structure of OxyR mutant from Porphyromonas gingivalis
ComponentsRedox-sensitive transcriptional activator OxyR
KeywordsTRANSCRIPTION REGULATOR / beta-alpha-barrels / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / cytosol
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 ...: / 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
LysR substrate-binding domain-containing protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSvintradze, D.V. / Wright, H.T. / Lewis, J.P.
Citation
Journal: 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.
#1: Journal: To be Published
Title: The iron-oxygen molecular switch in the anaerobic bacterium Porphyromonas gingivalis
Authors: Lewis, J.P. / Yanamandra, S. / Ghosh, A.K. / Svintradze, D.V. / Sengupta, D. / Jones, K. / Iyer, D. / Peterson, D. / Wright, H.T. / Anaya-Bergman, C.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Redox-sensitive transcriptional activator OxyR
B: Redox-sensitive transcriptional activator OxyR
C: Redox-sensitive transcriptional activator OxyR
D: Redox-sensitive transcriptional activator OxyR


Theoretical massNumber of molelcules
Total (without water)102,4224
Polymers102,4224
Non-polymers00
Water6,810378
1
A: Redox-sensitive transcriptional activator OxyR
B: Redox-sensitive transcriptional activator OxyR


Theoretical massNumber of molelcules
Total (without water)51,2112
Polymers51,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-7 kcal/mol
Surface area18830 Å2
MethodPISA
2
C: Redox-sensitive transcriptional activator OxyR
D: Redox-sensitive transcriptional activator OxyR


Theoretical massNumber of molelcules
Total (without water)51,2112
Polymers51,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-9 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.209, 64.356, 81.312
Angle α, β, γ (deg.)111.75, 90.56, 111.24
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Redox-sensitive transcriptional activator OxyR


Mass: 25605.510 Da / Num. of mol.: 4 / Fragment: Regulatory domain (UNP residues 90-308) / Mutation: C199S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: oxyR / Production host: Escherichia coli (E. coli) / References: UniProt: Q20K61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 30% PEG 3000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 23, 2011
RadiationMonochromator: MSC Varimax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→23.24 Å / Num. obs: 69702 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.53 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 0.9 / % possible all: 88.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
RESOLVEmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HO7

3ho7


Resolution: 2.2→18.358 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 31.7 / Stereochemistry target values: ML
Details: The structure factor file contains 69444 reflections with the resolution range of 1.90-23.24 A. However the resolution of 2.2-18.358 A with 44680 reflections was used for the refinement. The ...Details: The structure factor file contains 69444 reflections with the resolution range of 1.90-23.24 A. However the resolution of 2.2-18.358 A with 44680 reflections was used for the refinement. The decision of cutting the high resolution reflections was based on the low intensity signals for 1.90 A resolution which were keeping R factor high during the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 2272 5.09 %RANDOM
Rwork0.2339 ---
all0.2638 46952 --
obs0.236 44680 90.64 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.001 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7083 Å2-0.9649 Å20.2759 Å2
2--17.6209 Å2-5.5998 Å2
3---3.2645 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6725 0 0 378 7103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096857
X-RAY DIFFRACTIONf_angle_d1.2059264
X-RAY DIFFRACTIONf_dihedral_angle_d15.3092636
X-RAY DIFFRACTIONf_chiral_restr0.0781038
X-RAY DIFFRACTIONf_plane_restr0.0051197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27850.38811940.36374198X-RAY DIFFRACTION89
2.2785-2.36960.36922090.32024215X-RAY DIFFRACTION89
2.3696-2.47720.33042280.2814200X-RAY DIFFRACTION90
2.4772-2.60740.34142390.27884188X-RAY DIFFRACTION90
2.6074-2.77030.32912440.28234193X-RAY DIFFRACTION90
2.7703-2.98340.34952240.29384255X-RAY DIFFRACTION91
2.9834-3.2820.31242270.26694253X-RAY DIFFRACTION91
3.282-3.75340.28812240.23444280X-RAY DIFFRACTION91
3.7534-4.71560.20372510.18144301X-RAY DIFFRACTION93
4.7156-18.35830.24312320.19664325X-RAY DIFFRACTION92

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