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- PDB-6f5c: Structure of h. salinarum RosR (vng0258) grown from NaCl -

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Basic information

Entry
Database: PDB / ID: 6f5c
TitleStructure of h. salinarum RosR (vng0258) grown from NaCl
ComponentsHALOPHILIC WINGED-HELIX-TURN-HELIX DNA BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / HALOPHILES / WHTH DNA BINDING PROTEIN / ROSR / HIGH SALT MEDIUM
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / PadR family transcription regulator RosR
Function and homology information
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShaanan, B. / Kutnowski, N. / Shmuely, H.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1382/13 Israel
CitationJournal: J. Struct. Biol. / Year: 2018
Title: The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.
Authors: Kutnowski, N. / Shmuely, H. / Dahan, I. / Shmulevich, F. / Davidov, G. / Shahar, A. / Eichler, J. / Zarivach, R. / Shaanan, B.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3May 1, 2024Group: 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: HALOPHILIC WINGED-HELIX-TURN-HELIX DNA BINDING PROTEIN
B: HALOPHILIC WINGED-HELIX-TURN-HELIX DNA BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,09228
Polymers29,1102
Non-polymers98226
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer in solution according to gel filtration and SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-279 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.824, 71.350, 41.879
Angle α, β, γ (deg.)90.000, 110.749, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein HALOPHILIC WINGED-HELIX-TURN-HELIX DNA BINDING PROTEIN


Mass: 14554.919 Da / Num. of mol.: 2
Fragment: RESIDUES 1-10 IN BOTH CHAINS ARE PREDICTED TO BE NATIVELY DISORDERED. RESIDUES 70-76 IN BOTH CHAINS BELONG TO THE WING DOMAIN WHICH IS NOTORIOUSLY FLEXIBLE.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium salinarum NRC-1 (Halophile)
Gene: VNG_0258H / Production host: Haloferax volcanii (archaea) / References: UniProt: Q9HSF4
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.05 Å3/Da / Density % sol: 37.06 % / Description: Monoclinic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: NaCl, MES, Ammonium sulfate / PH range: 6-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.55→39.16 Å / Num. obs: 60536 / % possible obs: 94.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 20.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1023 / CC1/2: 0.53 / Rpim(I) all: 0.728 / Rrim(I) all: 0.941 / % possible all: 61.3

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Processing

Software
NameVersionClassification
REFMACversio 5.8refinement
PHENIX1.13rc1_2958refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD DERIVED MODEL IN NACL

Resolution: 1.55→39.16 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.63
Details: RESIDUES 1-10 IN BOTH CHAINS ARE PREDICTED TO BE NATIVELYDISRODERED. RESIDUES 70-76 IN BOTH CHAINS BELONG TO THE WING DOMAIN WHICH IS NOTORIOUSLY FLEXIBLE
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3050 5.04 %random
Rwork0.179 ---
obs0.18 60536 94.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.73 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 30 197 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041809
X-RAY DIFFRACTIONf_angle_d0.6792452
X-RAY DIFFRACTIONf_chiral_restr0.04275
X-RAY DIFFRACTIONf_plane_restr0.0034327
X-RAY DIFFRACTIONf_dihedral_angle_d12.80051102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.5740.284890.3291655X-RAY DIFFRACTION61.21
1.574-1.5990.3391240.3031903X-RAY DIFFRACTION70
1.599-1.6270.3481160.2942095X-RAY DIFFRACTION76
1.627-1.6570.3211080.2872317X-RAY DIFFRACTION83.05
1.657-1.6890.3131230.2712560X-RAY DIFFRACTION90.25
1.689-1.7230.2811320.2542656X-RAY DIFFRACTION97.45
1.723-1.7610.2961540.2472794X-RAY DIFFRACTION99.83
1.761-1.8020.2741520.2312742X-RAY DIFFRACTION99.83
1.802-1.8470.2151470.2292772X-RAY DIFFRACTION100
1.847-1.8970.2531450.2222797X-RAY DIFFRACTION99.9
1.897-1.9530.2431450.2062752X-RAY DIFFRACTION99.97
1.953-2.0160.1971480.1892755X-RAY DIFFRACTION100
2.016-2.0880.1841500.1812766X-RAY DIFFRACTION99.93
2.088-2.1710.21590.1732751X-RAY DIFFRACTION100
2.171-2.270.2171330.172791X-RAY DIFFRACTION100
2.27-2.390.21350.1622783X-RAY DIFFRACTION100
2.39-2.5390.2121280.172788X-RAY DIFFRACTION100
2.539-2.7350.181700.1672771X-RAY DIFFRACTION99.93
2.735-3.0110.1781530.1712744X-RAY DIFFRACTION100
3.011-3.4460.1981520.1682776X-RAY DIFFRACTION100
3.446-4.3410.1491650.1362744X-RAY DIFFRACTION100
4.341-39.160.2311220.1692774X-RAY DIFFRACTION99.04
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)
14.697489923711.476414685765.85194913251.535876731221.012350476127.98597164532-0.4344608461340.7249150550560.766512819804-0.260285201389-0.407916186387-0.341792144134-2.873763527710.7800778164510.970360208420.4651308465870.0492790314325-0.05356072719240.3188652691250.03986279760360.2534041363528.0908489778728.29842386914.94292936701
23.42543519274-0.03037958429760.4963850300957.08041629789-0.9716982638455.88789006552-0.104396790544-0.08579030508270.05144676760340.139102048154-0.011522368056-0.0352196456564-0.185501339344-0.02297409668990.1153025551330.09905206278450.00895869904464-0.01614060628930.127698038186-0.01101882089510.1063364945772.921336784625.750098988120.3770762574
34.022832995791.05345294693-2.370460560831.983608511340.06078481523283.765937744310.669880327477-0.815839001910.169617061131.22407452043-0.5343785512590.424862958534-1.313479940580.00944373486688-0.04250227549260.792465146038-0.1226336601290.02319115272480.363245846785-0.01953069676040.3671880596121.1760901664337.831388902423.5372052434
41.666643067810.4356690148260.2446932311633.027296588611.96148699333.67582549815-0.0513756427469-0.0175178549096-0.05029320639180.0354167411935-0.00572423809718-0.0418042251046-0.0816653873083-0.1914884444830.04402340360790.09179160076070.0546190860168-0.07097706761720.1561911899010.02025930952290.170577738223-6.257233841221.09786650754.90574574535
59.797711205936.08024806395-7.300957645865.48668994185-3.205780382656.74671789408-0.401962609492-2.24460860265-1.275848263230.512118281031-0.501883078601-0.1838151524330.6309685185450.7412988744530.7494765940780.2895726151570.02624891122960.06039888410410.373304988060.09473271184650.2891611784637.4944679228713.056974770813.4922063829
64.174197665141.58999804066-1.360784571537.165150490870.3050271349994.34686140009-0.04332003046510.09189749920930.0038274160021-0.1971810556190.1132962753980.143489632379-0.2119098139410.0243053766482-0.05684767099470.06005569660690.0133767933301-0.04203507663450.142289387530.01165807033810.11355359535310.501205350117.0725030299-3.46992552151
76.690375530937.28524621581-5.505483929438.40039899122-5.836904175718.688424813290.100088549191-0.242199913038-0.1894800167730.205831762336-0.338552659818-0.27737512387-0.0796077258920.8782335700170.196029421560.1060427670620.013422203985-0.03673307500230.2419395858280.004233798169890.20025017009918.058387354911.25577528162.23617676734
84.62964590519-0.0972667113872-2.53970737884.669258784831.871484225228.86539905269-0.04907858748350.830839179773-0.634029209322-0.437806843571-0.00834018255568-0.4150952854351.221485310560.0574981804960.04847761070940.3055392012890.04900551194780.02288620370470.300636064352-0.06716969422210.32569602879611.03138027591.6831493387-4.90904645564
92.22937432979-0.808189309768-1.195306424423.082616904671.643155983024.01696245932-0.132798078223-0.03645632830680.09051783747360.0280958446197-0.0100057414862-0.0100319041835-0.263878979674-0.3229136877630.1171461577060.073649675547-0.0338468655034-0.03464348974230.159404858849-0.0182240043930.192810810695-7.6016415903318.05758730874.58131844482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 120 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 16 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 49 )
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 62 )
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 81 )
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 120 )

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