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- PDB-6fdh: Structure of H. salinarum RosR (vng0258) grown from KCl -

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Basic information

Entry
Database: PDB / ID: 6fdh
TitleStructure of H. salinarum RosR (vng0258) grown from KCl
ComponentsDNA 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 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsShaanan, B. / Kutnowski, N.
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 23, 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

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Assembly

Deposited unit
A: DNA binding protein
B: DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91523
Polymers29,1102
Non-polymers80521
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-252 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.069, 76.966, 42.129
Angle α, β, γ (deg.)90.000, 110.210, 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 DNA binding protein


Mass: 14554.919 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WINGED HELIX-TURN-HELIX 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: (gene. exp.) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / 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.: 20 / 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.: 199 / 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: 2.15 Å3/Da / Density % sol: 42.7 % / Description: Monoclinic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: KCL, AMMONIUM SULFATE, MES PH 6.8 / PH range: 6.0-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9219 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 16, 2013 / Details: MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9219 Å / Relative weight: 1
ReflectionResolution: 1.85→39.5 Å / Num. obs: 21011 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.036 / Rrim(I) all: 0.086 / Net I/σ(I): 17.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 5.67 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1277 / CC1/2: 0.522 / Rpim(I) all: 0.827 / Rrim(I) all: 0.85 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.13rc2_2986refinement
REFMACv 5.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD derived model in NaCl

Resolution: 1.85→38.54 Å / SU ML: 0.2291 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 22.0575
Details: 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 995 4.74 %Random
Rwork0.1791 ---
obs0.1811 20985 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.54 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 25 199 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631800
X-RAY DIFFRACTIONf_angle_d0.77722439
X-RAY DIFFRACTIONf_chiral_restr0.043274
X-RAY DIFFRACTIONf_plane_restr0.0039325
X-RAY DIFFRACTIONf_dihedral_angle_d10.38961093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.950.30311510.25992824X-RAY DIFFRACTION99.37
1.95-2.070.27281320.20062848X-RAY DIFFRACTION99.6
2.07-2.230.23891340.19392833X-RAY DIFFRACTION99.56
2.23-2.450.24821280.18172872X-RAY DIFFRACTION99.87
2.45-2.810.24831620.18662851X-RAY DIFFRACTION99.9
2.81-3.540.20781490.17442854X-RAY DIFFRACTION99.97
3.54-38.550.17541390.15712908X-RAY DIFFRACTION99.84
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)
14.965300474161.54959232282-5.036974052373.02726299781-0.8978361300065.28902772297-0.001947472815981.75274674323-2.13186978449-1.88068842076-0.701082843098-0.1896657086941.70486831892-0.8904421564770.6363940012950.632198331853-0.06106574124230.0585453416920.468272628108-0.01754429774590.499243134129-2.60699488422-26.6100299392-18.6845034796
25.82958870804-1.841318900252.397166389634.65799915049-2.6357229554.758712176590.1090833144050.0516303431541-0.235485771344-0.060559331437-0.0312231355731-0.205693653882-0.02105258778060.478900287911-0.08270990761990.159920056071-0.009976846559140.02680808219190.193346114421-0.02046856956460.222006920528-4.17058723746-24.6779925514-4.26862179057
35.354367857372.18841428632-1.400121167957.913399936172.477002424742.555642559060.00768319561207-0.1846653676630.02676016913270.285727360848-0.08244453518310.170413255435-0.134205954359-0.04025438365810.09449297171150.1581537832070.0170853649144-0.01379916401320.1687034262420.02988684607390.112729014723-11.275941897-20.37512437420.531997806324
42.699932154360.8457640272171.32795856054.957944557781.320253834963.043193707090.151824671704-0.294319936162-0.7440258055210.04589176807090.2057859842150.7082365810.46970785383-0.605791649856-0.1608459704110.250321075091-0.02614684575670.04991290663610.2669580023880.0522281748850.436819747617-11.4200063555-34.4785195117-4.06449078323
50.193992542906-0.05843121201210.3804666585920.0253178309915-0.128758314530.770769135066-0.362087636898-0.337298570127-0.806539575431.03320844559-0.2280252072350.4126567406070.252948608636-0.8354662837940.589973643780.568100170188-0.1860264638120.08952590782410.7911977816020.1410360551220.743679340294-18.4679069367-33.38178110036.82933603955
67.867392497813.34660947237-4.206968368373.70967970329-2.602670501574.47607568578-0.3314869165190.426604006689-0.464607304127-0.1603425722680.147708650874-0.06889339771490.3387656822130.01639051938550.156783644520.192390842440.0187430660003-0.0334512789210.196371638533-0.02564897720580.2482118506931.54465609597-29.4204525925-9.16430699619
73.43272640834-0.4337264237491.93964683483.2764556655-0.1469327693377.44148961867-0.201599200463-0.1800974590670.1462547753370.101213491502-0.0635179563168-0.226787692571-0.3801716918520.3680838629820.2615787009020.176871184623-0.0463507876853-0.01631897146120.2953050480360.00232892658590.23274946343815.3572890754-15.8590803221-5.99892135089
87.893211869692.168237428685.17363379414.64240598355-1.883201726856.08910730480.0624266272705-0.6663307123550.667511130320.210386710931-0.3056678346070.243215652816-1.01261941499-1.083914775580.2497518717640.3288117473280.03183503811870.07435503269510.265482372685-0.03600916467210.27731631165-5.02531726911-11.3473754967-12.1246301912
93.5049941411-2.065579468974.099450961637.66260905358-1.548651450755.01868259995-0.1902738146550.169866627844-0.01715317821320.09980872736-0.116566047248-0.33249947744-0.0176654745250.535501751610.283361832230.233888409763-0.01851120993170.01618395882250.131344252020.008810436676650.1463694102046.31291451228-11.0876023487-20.7281890298
104.30323883753.24835936181-1.094856514956.50873712433-2.825335454584.8065890238-0.174293047350.1328164080710.0102293322326-0.2718374926710.229906063637-0.366817188148-0.02654187709620.154138099533-0.07986863097640.202399711679-0.006094638044240.0280184487830.1828214768350.00249849636150.1759277469322.91822189005-17.5848507984-26.5190633451
114.103592846750.4344173229310.6700008006019.31545881244.153967180576.44257943966-0.04934674013720.3523891265910.307450780964-0.283410006317-0.1731434611670.346120196596-0.614648627305-0.4877659733380.2182216985470.2687505144070.05645975585990.04062561357810.2379044279050.04183013948640.202634127865-3.46717598222-7.87438220301-23.7422134874
124.255125072663.29041305346-3.948131428299.72716855537-1.752607360323.91158812645-0.5349588517690.787051793199-0.00125458473477-1.802791193830.2457436217321.116067120770.0291500656502-1.734047153560.1479764097420.5883890904250.0211010143146-0.1189692435390.5377119652970.06567671482610.5528588171684.955022312441.88714133334-35.4321084415
133.32249054328-0.0793456836750.6631871195815.35834164011-3.313388812612.165440266440.0723923318183-0.1667055880280.2970966362490.1929671527160.04137986199860.0754434738688-0.8949281570130.193345603616-0.05208364216750.285453182914-0.0325152422447-0.01296229445140.159672041486-0.02984205355360.2397566850445.31662166313-4.90883183838-16.0443166956
146.96885328699-0.678467464623-2.139929550473.3658472768-0.5322683915974.30240788068-0.06480260285510.0755294720582-0.222946417921-0.00837423693507-0.00567792020385-0.04202413186870.01991488201530.1783107240920.06844407778540.147246051897-0.0242461962151-0.04363812625590.227895479204-0.02683470091090.19877543259312.1794453678-23.3540267365-5.42333804443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 11:14)
2X-RAY DIFFRACTION2(chain A and resid 15:31)
3X-RAY DIFFRACTION3(chain A and resid 32:57)
4X-RAY DIFFRACTION4(chain A and resid 58:72)
5X-RAY DIFFRACTION5(chain A and resid 73:76)
6X-RAY DIFFRACTION6(chain A and resid 77:95)
7X-RAY DIFFRACTION7(chain A and resid 96:120)
8X-RAY DIFFRACTION8(chain B and resid 11:19)
9X-RAY DIFFRACTION9(chain B and resid 20:32)
10X-RAY DIFFRACTION10(chain B and resid 33:45)
11X-RAY DIFFRACTION11(chain B and resid 46:69)
12X-RAY DIFFRACTION12(chain B and resid 70:74)
13X-RAY DIFFRACTION13(chain B and resid 75:90)
14X-RAY DIFFRACTION14(chain B and resid 91:120)

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