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- PDB-6g1d: Corynebacterium glutamicum OxyR C206 mutant -

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Basic information

Entry
Database: PDB / ID: 6g1d
TitleCorynebacterium glutamicum OxyR C206 mutant
ComponentsHydrogen peroxide-inducible genes activator
KeywordsTRANSCRIPTION / Hydrogen peroxide / redox / transcription factor / LysR
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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FORMIC ACID / FORMYL GROUP / DI(HYDROXYETHYL)ETHER / : / Probable hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 Å
AuthorsYoung, D.R. / Pedre, B.P. / Messens, J.M.
Funding support Belgium, Spain, 7items
OrganizationGrant numberCountry
VIB Belgium
IWT Belgium
HerculesHERC16 Belgium
FWOG.0D79.14N Belgium
VUB Strategic Research ProgrammeSRP34 Belgium
Junta de Castilla y LeonLE326U14 Spain
University of LeonUXXI2016/00127 Spain
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2sensing.
Authors: Pedre, B. / Young, D. / Charlier, D. / Mourenza, A. / Rosado, L.A. / Marcos-Pascual, L. / Wahni, K. / Martens, E. / G de la Rubia, A. / Belousov, V.V. / Mateos, L.M. / Messens, J.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
C: Hydrogen peroxide-inducible genes activator
D: Hydrogen peroxide-inducible genes activator
B: Hydrogen peroxide-inducible genes activator
A: Hydrogen peroxide-inducible genes activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,35920
Polymers141,2014
Non-polymers1,15816
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-142 kcal/mol
Surface area53640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.409, 63.481, 157.414
Angle α, β, γ (deg.)90.000, 97.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules CDBA

#1: Protein
Hydrogen peroxide-inducible genes activator


Mass: 35300.230 Da / Num. of mol.: 4 / Mutation: C206S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: C0I99_13405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H5I9R9, UniProt: Q8NP91*PLUS

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Non-polymers , 7 types, 684 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Mutation: C206S
Source method: isolated from a genetically manipulated source
Formula: C2H6O2 / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Mutation: C206S
Source method: isolated from a genetically manipulated source
Formula: CH2O2 / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Mutation: C206S
Source method: isolated from a genetically manipulated source
Formula: Na / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Production host: Escherichia coli (E. coli)
#7: Chemical ChemComp-FOR / FORMYL GROUP / Aldehyde


Mass: 30.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, 2-(N-morpholino)ethanesulfonic acid (MES), lithium sulfate, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98015 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98015 Å / Relative weight: 1
ReflectionResolution: 1.99→49.23 Å / Num. obs: 98727 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 40.57 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.34 / Rpim(I) all: 0.138 / Rrim(I) all: 0.367 / Net I/σ(I): 2.8 / Num. measured all: 692313 / Scaling rejects: 532
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.99-2.036.11.88241320.30.7892.04685.1
10.91-49.236.70.2016580.9440.0820.21799.1

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x6g

4x6g


Resolution: 1.992→44.864 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.2212 4916 4.98 %
Rwork0.1998 --
obs0.2009 98622 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.21 Å2 / Biso mean: 50.2316 Å2 / Biso min: 18.29 Å2
Refinement stepCycle: final / Resolution: 1.992→44.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9430 0 116 668 10214
Biso mean--41.39 55.33 -
Num. residues----1253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149922
X-RAY DIFFRACTIONf_angle_d1.66413554
X-RAY DIFFRACTIONf_chiral_restr0.1051655
X-RAY DIFFRACTIONf_plane_restr0.011754
X-RAY DIFFRACTIONf_dihedral_angle_d14.6586122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.992-2.01460.36891290.37052348247776
2.0146-2.03830.35841690.34333119328899
2.0383-2.06320.33471650.33013120328599
2.0632-2.08930.30651590.31373070322999
2.0893-2.11680.29451650.30663158332399
2.1168-2.14580.3061420.29253091323399
2.1458-2.17640.34011670.28813178334599
2.1764-2.20890.31111490.2833075322499
2.2089-2.24340.31431840.27343106329099
2.2434-2.28020.25961650.25523142330799
2.2802-2.31950.2581710.24913127329899
2.3195-2.36170.28611620.23043100326299
2.3617-2.40710.22451650.21913143330899
2.4071-2.45620.24811540.21863174332899
2.4562-2.50960.23621610.222731053266100
2.5096-2.5680.24921620.22483179334199
2.568-2.63220.2581690.222131233292100
2.6322-2.70340.26171700.213231033273100
2.7034-2.78290.24811720.216631633335100
2.7829-2.87270.25511840.210831543338100
2.8727-2.97540.26231550.215531773332100
2.9754-3.09450.25131800.203331163296100
3.0945-3.23530.23761490.203331793328100
3.2353-3.40580.24241670.192231673334100
3.4058-3.61910.22971700.189231583328100
3.6191-3.89840.19461760.176131823358100
3.8984-4.29040.16761590.159731983357100
4.2904-4.91060.1611760.151732163392100
4.9106-6.18430.18561510.17232253376100
6.1843-44.87510.16221690.176633103479100
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)
11.7082-0.294-0.56663.13820.77310.7363-0.06720.4053-0.11280.7310.513-0.57450.45740.6024-0.39660.47980.1398-0.15520.5874-0.11370.504614.82047.193871.4694
20.7564-0.2886-0.93420.270.02861.7340.0632-0.10750.1897-0.01150.03970.00560.06610.2433-0.16030.3479-0.0511-0.00340.4617-0.04310.388-13.172829.2128107.1736
32.6198-0.2374-1.23110.76060.41822.94650.14610.11380.3439-0.0487-0.0068-0.014-0.12270.0923-0.18890.3157-0.03440.01070.2866-0.01630.375-21.44436.479106.1339
43.6541-0.4977-0.05063.13970.74593.8240.1822-0.03550.50960.11680.2264-0.17670.07060.5565-0.31040.34790.0020.04350.5072-0.04860.37799.863529.877480.6659
51.8344-0.1928-0.02121.32110.56743.15730.0669-0.0341-0.1427-0.0336-0.03570.10120.1316-0.2588-0.03620.3386-0.0387-0.00140.36310.02140.423122.95314.0611117.9594
64.49771.76490.53563.6259-0.47533.50190.1881-0.1521-0.46140.2892-0.0927-0.47460.37520.6302-0.08320.51010.0797-0.09250.6768-0.01030.4542-1.62112.0776154.4923
70.54040.8450.02336.79331.26483.1994-0.12280.25480.0622-0.20920.4384-0.4424-0.51550.3688-0.3150.46120.02310.00050.5587-0.06020.3478-2.193225.4341146.8805
82.43070.0799-0.92611.9352-0.76491.92830.228-0.4428-0.15360.2809-0.2034-0.034-0.0203-0.1296-0.01330.4373-0.11360.00620.5237-0.04550.42413.750325.2051132.6271
91.84030.1877-0.8310.59990.29242.20240.01480.1360.2184-0.0491-0.00250.14840.0453-0.2362-0.00320.3298-0.02460.01960.3709-0.00590.440920.037829.8063111.9443
102.44590.2164-0.29641.22310.6931.55560.1603-0.45720.61180.2265-0.21580.0969-0.0924-0.1907-0.07130.3679-0.0480.07190.446-0.10380.493717.623736.0206128.0724
113.2462-0.4401-0.98391.7219-0.07242.45130.06340.05540.2366-0.36170.0764-0.1203-0.31620.1148-0.11160.5059-0.035-0.00590.5225-0.05940.3979-8.355638.9198161.5635
121.24191.3161-0.04256.23921.08690.92070.2414-0.01510.2102-0.4231-0.23860.3305-0.311-0.0333-0.02490.64480.0087-0.00910.5311-0.04670.4174-10.715930.1828149.5733
131.12610.01530.70250.97570.50962.8704-0.06330.0065-0.08460.02160.013-0.07220.01150.1650.02010.3314-0.0159-0.00360.3909-0.01030.4065-14.89389.1533118.4742
144.20920.1786-1.59130.2097-0.80813.592-0.25090.0455-0.0549-0.2595-0.0356-0.62760.63710.33550.25770.51390.04510.05830.5598-0.0440.4379-7.35897.2418103.2534
151.1582-0.04950.27410.7013-0.15632.1597-0.04650.088-0.01270.00520.0448-0.07370.06460.0162-0.0390.2916-0.01270.0130.3493-0.020.3326-18.30718.4409110.6121
162.3997-0.71380.73981.25780.00522.93010.0455-0.2606-0.0890.0754-0.13050.03140.5379-0.2888-0.01590.3823-0.05170.00620.3480.02980.3955-23.80432.8165122.158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 4 through 65 )C4 - 65
2X-RAY DIFFRACTION2chain 'C' and (resid 66 through 259 )C66 - 259
3X-RAY DIFFRACTION3chain 'C' and (resid 260 through 322 )C260 - 322
4X-RAY DIFFRACTION4chain 'D' and (resid -1 through 92 )D-1 - 92
5X-RAY DIFFRACTION5chain 'D' and (resid 93 through 323 )D93 - 323
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 65 )B4 - 65
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 94 )B66 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 145 )B95 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 276 )B146 - 276
10X-RAY DIFFRACTION10chain 'B' and (resid 277 through 326 )B277 - 326
11X-RAY DIFFRACTION11chain 'A' and (resid 5 through 65 )A5 - 65
12X-RAY DIFFRACTION12chain 'A' and (resid 66 through 91 )A66 - 91
13X-RAY DIFFRACTION13chain 'A' and (resid 92 through 205 )A92 - 205
14X-RAY DIFFRACTION14chain 'A' and (resid 206 through 234 )A206 - 234
15X-RAY DIFFRACTION15chain 'A' and (resid 235 through 290 )A235 - 290
16X-RAY DIFFRACTION16chain 'A' and (resid 291 through 322 )A291 - 322

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