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- PDB-5b7d: OxyR2 E204G mutant regulatory domain from Vibrio vulnificus (sulf... -

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Basic information

Entry
Database: PDB / ID: 5b7d
TitleOxyR2 E204G mutant regulatory domain from Vibrio vulnificus (sulfate-bound)
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / 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
Hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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
DepositionJun 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Nov 8, 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)48,4405
Polymers48,1522
Non-polymers2883
Water12,250680
1
A: LysR family transcriptional regulator
hetero molecules

A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3444
Polymers48,1522
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3440 Å2
ΔGint-82 kcal/mol
Surface area19040 Å2
MethodPISA
2
B: LysR family transcriptional regulator
hetero molecules

B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5366
Polymers48,1522
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3190 Å2
ΔGint-58 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.705, 137.238, 96.655
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: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium sulfate, 0.1M sodium citrate (pH 5.6), 11% PEG 4000, 2mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 74251 / % possible obs: 99.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.39
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6U

5b6u
PDB Unreleased entry


Resolution: 1.52→19.756 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 15.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1831 3644 5 %
Rwork0.1573 --
obs0.1586 72860 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→19.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 15 680 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083520
X-RAY DIFFRACTIONf_angle_d0.9644807
X-RAY DIFFRACTIONf_dihedral_angle_d4.033331
X-RAY DIFFRACTIONf_chiral_restr0.066570
X-RAY DIFFRACTIONf_plane_restr0.006633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5201-1.54010.22691100.20122026X-RAY DIFFRACTION76
1.5401-1.56120.2402950.20812377X-RAY DIFFRACTION87
1.5612-1.58350.2321390.20792520X-RAY DIFFRACTION93
1.5835-1.60710.23011310.20522564X-RAY DIFFRACTION96
1.6071-1.63220.23711330.20712660X-RAY DIFFRACTION98
1.6322-1.6590.2441550.19592651X-RAY DIFFRACTION99
1.659-1.68760.23981220.18972678X-RAY DIFFRACTION99
1.6876-1.71820.19611500.18252680X-RAY DIFFRACTION99
1.7182-1.75130.21911360.18232695X-RAY DIFFRACTION100
1.7513-1.7870.19521430.18532686X-RAY DIFFRACTION100
1.787-1.82580.20991480.17412702X-RAY DIFFRACTION100
1.8258-1.86830.20441390.16782679X-RAY DIFFRACTION100
1.8683-1.91490.18691450.15322696X-RAY DIFFRACTION100
1.9149-1.96670.17291450.15442708X-RAY DIFFRACTION100
1.9667-2.02450.16571390.15092697X-RAY DIFFRACTION100
2.0245-2.08980.19371590.15072691X-RAY DIFFRACTION100
2.0898-2.16440.17261470.14222700X-RAY DIFFRACTION100
2.1644-2.25090.16411560.14062705X-RAY DIFFRACTION100
2.2509-2.35320.16631270.14452751X-RAY DIFFRACTION100
2.3532-2.4770.16261360.1472723X-RAY DIFFRACTION100
2.477-2.63190.19661640.15222703X-RAY DIFFRACTION100
2.6319-2.83460.17521640.15742708X-RAY DIFFRACTION100
2.8346-3.11880.1761450.15242760X-RAY DIFFRACTION100
3.1188-3.56780.16751500.14662750X-RAY DIFFRACTION100
3.5678-4.48640.14881390.13222789X-RAY DIFFRACTION100
4.4864-19.75750.18781270.15472917X-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)
14.7851-2.00780.97150.8666-0.41280.20090.09750.45560.2191-0.0063-0.15-0.19290.01130.1730.03640.0891-0.01890.00160.17570.02420.146326.9473-6.340716.951
21.13910.2109-0.0260.4157-0.04270.8114-0.020.00010.0005-0.0470.0020.0021-0.04770.0480.01810.0957-0.00190.00140.0658-0.00490.06136.6268-5.987213.1672
31.4392-0.82530.10060.94230.01613.08330.03240.1486-0.1544-0.0831-0.02830.1741-0.1517-0.31590.04330.09310.0137-0.02440.1118-0.00040.1077-16.0707-4.971511.0065
40.82940.226-0.42520.5138-0.24020.6911-0.05390.0876-0.0678-0.08360.0075-0.04250.0279-0.01790.04730.0988-0.0036-0.00770.0828-0.00990.06640.658-10.635911.8419
53.5781-1.78920.10180.897-0.0521-0.00220.07460.3096-0.41980.0167-0.09870.21-0.0155-0.1681-0.02090.0989-0.02950.0120.2237-0.04710.1759-28.0709-41.509917.3913
61.1210.4647-0.11010.6907-0.04040.9281-0.05120.071-0.0259-0.06130.03070.02270.0943-0.10670.0220.0824-0.0144-0.00190.0856-0.01030.0745-8.3486-41.906914.1991
72.8461-0.635-0.96890.2482-0.25532.90150.07950.0946-0.018-0.0869-0.0536-0.05130.14430.24910.03110.12280.03130.03460.1022-0.01360.106714.5207-42.829.3607
81.19910.34880.24350.67740.08110.7141-0.03850.14970.0562-0.07380.00820.07170.0646-0.02920.03090.0694-0.00610.00830.07860.00160.0573-2.1421-37.142111.8548
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 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 180 )
7X-RAY DIFFRACTION7chain 'B' and (resid 181 through 230 )
8X-RAY DIFFRACTION8chain 'B' and (resid 231 through 301 )

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