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- PDB-5x0q: OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 5x0q
TitleOxyR2 E204G variant (Cl-bound) 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
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.2Nov 22, 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
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)48,4155
Polymers48,1522
Non-polymers2633
Water10,917606
1
A: LysR family transcriptional regulator
hetero molecules

A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2224
Polymers48,1522
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2990 Å2
ΔGint-39 kcal/mol
Surface area18630 Å2
MethodPISA
2
B: LysR family transcriptional regulator
hetero molecules

B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6076
Polymers48,1522
Non-polymers4554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3500 Å2
ΔGint-38 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.213, 138.232, 97.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-163-

GLU

21A-767-

HOH

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Components

#1: Protein LysR family transcriptional regulator / OxyR


Mass: 24075.781 Da / Num. of mol.: 2 / Fragment: UNP residues 86-301 / Mutation: E204G
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.: 606 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium citrate (pH 6.5), 14% PEG 3350, 2mM TCEP (Tris(2carboxyethyl)phosphine), 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.0082 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0082 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 69247 / % possible obs: 99.4 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.028 / Net I/σ(I): 19.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.17 / Num. unique all: 3289 / Rpim(I) all: 0.163 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B7D

5b7d


Resolution: 1.55→19.868 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 16.92
RfactorNum. reflection% reflection
Rfree0.1876 3199 4.96 %
Rwork0.1549 --
obs0.1565 64561 92.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 15 606 3901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123469
X-RAY DIFFRACTIONf_angle_d1.2094729
X-RAY DIFFRACTIONf_dihedral_angle_d4.792930
X-RAY DIFFRACTIONf_chiral_restr0.078566
X-RAY DIFFRACTIONf_plane_restr0.008615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57310.2499680.19981609X-RAY DIFFRACTION56
1.5731-1.59770.2407950.20221831X-RAY DIFFRACTION64
1.5977-1.62390.2293860.20972005X-RAY DIFFRACTION70
1.6239-1.65190.22381130.20172205X-RAY DIFFRACTION77
1.6519-1.68190.24371440.18742422X-RAY DIFFRACTION86
1.6819-1.71420.22111260.19052595X-RAY DIFFRACTION91
1.7142-1.74920.18441480.1812690X-RAY DIFFRACTION95
1.7492-1.78720.21931410.18722761X-RAY DIFFRACTION97
1.7872-1.82880.23031600.17942834X-RAY DIFFRACTION99
1.8288-1.87450.23221400.16922821X-RAY DIFFRACTION99
1.8745-1.92510.2021420.16062826X-RAY DIFFRACTION99
1.9251-1.98170.18551440.14752867X-RAY DIFFRACTION100
1.9817-2.04560.18011520.14652853X-RAY DIFFRACTION100
2.0456-2.11860.17781360.14552872X-RAY DIFFRACTION100
2.1186-2.20340.1691670.14452856X-RAY DIFFRACTION100
2.2034-2.30350.17881620.1392879X-RAY DIFFRACTION100
2.3035-2.42480.18711370.14612867X-RAY DIFFRACTION100
2.4248-2.57640.1891610.1532879X-RAY DIFFRACTION100
2.5764-2.77480.17871390.15582914X-RAY DIFFRACTION100
2.7748-3.05320.19361580.15692879X-RAY DIFFRACTION100
3.0532-3.49290.18911480.14722919X-RAY DIFFRACTION100
3.4929-4.39280.16461570.13062941X-RAY DIFFRACTION100
4.3928-19.86920.15851750.14813037X-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)
11.4548-1.06140.6160.6245-0.36470.248-0.06630.5430.1943-0.01-0.0697-0.22860.02670.2420.04130.0656-0.0012-0.00390.17270.0130.132726.3257-6.324416.9387
21.00960.1707-0.35740.7759-0.10280.8913-0.05930.015-0.029-0.08210.0151-0.0180.0143-0.02580.02980.0629-0.0102-0.00750.0505-0.00420.03256.7533-5.927413.2779
31.0484-0.3913-0.06491.2497-0.44071.2931-0.01250.289-0.0325-0.1512-0.01920.1889-0.0889-0.2830.0120.0811-0.0002-0.03960.1735-0.02010.0788-13.7755-6.732413.7243
40.7650.205-0.62171.2649-0.22720.9056-0.18260.205-0.1345-0.26880.0621-0.13830.1457-0.0750.01340.1129-0.0251-0.01480.1099-0.00940.03964.8602-10.41898.8891
53.0455-1.6287-0.23920.73230.0348-0.00070.10460.3834-0.4446-0.0007-0.11540.2585-0.0289-0.2171-0.04580.094-0.01590.0130.1933-0.03590.1785-27.3383-41.819417.6697
61.39530.46490.20150.956-0.00790.6763-0.01210.05410.0324-0.118-0.00330.050.0229-0.00960.00960.0791-0.0011-0.00270.06-0.00590.0501-7.6819-41.712214.3577
72.0651-0.1926-0.29670.31330.15571.95180.03580.269-0.0395-0.2866-0.0576-0.20270.2330.16720.06330.16050.0340.07670.1398-0.00430.137613.212-44.02689.7167
80.90920.44770.46010.91280.01120.3301-0.07260.16180.1033-0.13420.03270.07310.01390.03960.02610.09090.00070.01650.08510.00970.052-2.1879-37.376512.0323
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 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 253 )
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 301 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 105 )
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 183 )
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 230 )
8X-RAY DIFFRACTION8chain 'B' and (resid 231 through 301 )

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