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- PDB-5x0v: Reduced form of regulatory domain of OxyR2 from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5x0v
TitleReduced form of regulatory domain of OxyR2 from Vibrio vulnificus
ComponentsLysR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / LysR-type transcription regulator / LTTR / OxyR / H2O2
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity / DNA binding
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
CITRIC ACID / Hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsJo, I. / Ha, N.-C.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The hydrogen peroxide hypersensitivity of OxyR2 in Vibrio vulnificus depends on conformational constraints
Authors: Jo, I. / Kim, D. / Bang, Y.-J. / Ahn, J. / Choi, S.H. / Ha, N.-C.
History
DepositionJan 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5595
Polymers48,2962
Non-polymers2633
Water7,927440
1
A: LysR family transcriptional regulator
hetero molecules

A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3674
Polymers48,2962
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3030 Å2
ΔGint-41 kcal/mol
Surface area18940 Å2
MethodPISA
2
B: LysR family transcriptional regulator
hetero molecules

B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7516
Polymers48,2962
Non-polymers4554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3440 Å2
ΔGint-42 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.204, 138.348, 97.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LysR family transcriptional regulator / OxyR2


Mass: 24147.844 Da / Num. of mol.: 2 / Fragment: UNP residues 86-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: MO6-24/O / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087I947
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 49.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium citrate (pH 6.5), 14% (w/v) PEG 3350, 2mM TCEP (Tris(2-carboxyethyl)phosphine), 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 62093 / % possible obs: 98.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.027 / Net I/σ(I): 18.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.45 / Num. unique all: 2958 / Rpim(I) all: 0.164 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→48.736 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 17.74
RfactorNum. reflection% reflection
Rfree0.1916 2869 5.16 %
Rwork0.1593 --
obs0.161 55578 88.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→48.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 15 440 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153459
X-RAY DIFFRACTIONf_angle_d1.314717
X-RAY DIFFRACTIONf_dihedral_angle_d5.7922941
X-RAY DIFFRACTIONf_chiral_restr0.095562
X-RAY DIFFRACTIONf_plane_restr0.008620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5992-1.62680.2523630.20231130X-RAY DIFFRACTION39
1.6268-1.65640.2118730.21361451X-RAY DIFFRACTION49
1.6564-1.68820.2656950.20261696X-RAY DIFFRACTION58
1.6882-1.72270.2381170.20162019X-RAY DIFFRACTION69
1.7227-1.76010.22451170.19952376X-RAY DIFFRACTION79
1.7601-1.80110.23861390.1972618X-RAY DIFFRACTION88
1.8011-1.84610.21581340.19782802X-RAY DIFFRACTION95
1.8461-1.8960.23661550.1822853X-RAY DIFFRACTION97
1.896-1.95180.2151410.17962908X-RAY DIFFRACTION98
1.9518-2.01480.20591830.16082894X-RAY DIFFRACTION99
2.0148-2.08680.19791670.15532933X-RAY DIFFRACTION99
2.0868-2.17040.191630.14692952X-RAY DIFFRACTION99
2.1704-2.26920.1821590.14522965X-RAY DIFFRACTION99
2.2692-2.38880.19191550.14942953X-RAY DIFFRACTION99
2.3888-2.53850.20371710.1512946X-RAY DIFFRACTION99
2.5385-2.73450.22421460.15833020X-RAY DIFFRACTION100
2.7345-3.00960.1721630.15923003X-RAY DIFFRACTION100
3.0096-3.4450.18281530.15463022X-RAY DIFFRACTION100
3.445-4.33990.14462020.1383018X-RAY DIFFRACTION100
4.3399-48.75910.1861730.14693150X-RAY DIFFRACTION100
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)
13.3814-1.62311.06520.7747-0.51210.33840.09540.538-0.0559-0.0691-0.1572-0.2850.06180.2847-0.00160.07160.0009-0.01460.1830.00250.186526.2746-6.44816.6062
21.03130.271-0.22520.9226-0.04051.0331-0.05250.0306-0.0436-0.11140.0191-0.03290.0039-0.0230.01850.0614-0.0083-0.00860.0491-0.00890.04846.1774-6.191513.2839
30.6354-0.58180.02810.6176-0.3831.53610.07740.3064-0.1172-0.1717-0.01630.2722-0.0505-0.40220.08750.1170.009-0.06380.23090.00360.1529-16.1168-4.922411.7358
40.45980.1557-0.13320.8022-0.01160.6963-0.11190.1894-0.0926-0.14010.032-0.02420.0763-0.08690.02820.0825-0.0171-0.01640.0821-0.01270.05790.1172-10.883112.0662
56.4101-2.2864-0.75470.81320.26830.0880.09920.6318-0.11260.0566-0.16190.29530.0301-0.22650.02130.1024-0.02250.01680.1733-0.03370.2391-27.3974-41.61417.6302
61.6125-0.1744-0.26031.74790.66771.39180.01350.03950.1668-0.1513-0.0360.1791-0.0757-0.09190.01890.0781-0.0183-0.01140.0552-0.01080.0891-12.7981-40.847918.2603
72.7751.52410.20771.91510.10190.6127-0.03670.2071-0.0551-0.21340.0251-0.02450.04580.05750.00730.12550.00290.00830.08250.00510.0612-2.2776-42.298810.5144
80.94840.1854-0.23420.0518-0.17921.57220.03970.3372-0.0207-0.3153-0.0283-0.24710.18460.24320.12420.19640.02480.11130.2047-0.00760.168414.2643-43.10529.648
90.61850.37630.23061.0046-0.11670.3411-0.0830.22830.1879-0.1730.02620.09050.01850.04680.02340.1184-0.00270.01360.10030.02340.0871-1.8384-37.104712.23
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 301 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 105 )
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 180 )
8X-RAY DIFFRACTION8chain 'B' and (resid 181 through 230 )
9X-RAY DIFFRACTION9chain 'B' and (resid 231 through 301 )

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