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- PDB-6faq: Structure of H. salinarum RosR (vng0258) grown from KBr -

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Basic information

Entry
Database: PDB / ID: 6faq
TitleStructure of H. salinarum RosR (vng0258) grown from KBr
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 / BROMIDE ION / PadR family transcription regulator RosR
Function and homology information
Biological speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 16, 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)30,96425
Polymers29,1102
Non-polymers1,85423
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Dimer in solution according to gel filtration and SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-34 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.149, 76.406, 42.098
Angle α, β, γ (deg.)90.000, 109.472, 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: Halobacterium salinarum NRC-1
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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Br / 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.: 189 / 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: 2.14 Å3/Da / Density % sol: 42.61 % / Description: Monoclinic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: KBR, MES, AMMONIUM SULFATE, PH 6.8, EVAPORATION, TEMPERATURE 298K
PH range: 6-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91508 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 15, 2013 / Details: Monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91508 Å / Relative weight: 1
ReflectionResolution: 1.95→39.69 Å / Num. obs: 33425 / % possible obs: 94.1 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.041 / Rrim(I) all: 0.112 / Net I/av σ(I): 5.4 / Net I/σ(I): 12.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 5717 / CC1/2: 0.797 / Rpim(I) all: 0.73 / Rrim(I) all: 0.88 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
PHENIX1.13rc2_2986refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD DERIVED MODEL IN NACL

Resolution: 1.95→38.2 Å / SU ML: 0.2862 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.9923
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
Rfree0.2358 1527 4.59 %Random
Rwork0.1886 ---
obs0.1908 33245 93.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.09 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 27 190 1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151816
X-RAY DIFFRACTIONf_angle_d0.35582462
X-RAY DIFFRACTIONf_chiral_restr0.0319275
X-RAY DIFFRACTIONf_plane_restr0.0023330
X-RAY DIFFRACTIONf_dihedral_angle_d6.45191108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.34531850.31763052X-RAY DIFFRACTION98.99
2.01-2.080.2751360.24023053X-RAY DIFFRACTION99.63
2.08-2.170.2531480.23053075X-RAY DIFFRACTION99.94
2.17-2.260.2815740.22981532X-RAY DIFFRACTION98.35
2.26-2.380.2582970.21582637X-RAY DIFFRACTION98.38
2.38-2.530.25671510.20293069X-RAY DIFFRACTION99.94
2.53-2.730.24661550.20443069X-RAY DIFFRACTION99.91
2.73-30.27021180.2043126X-RAY DIFFRACTION99.88
3-3.440.23551660.18493020X-RAY DIFFRACTION99.78
3.44-4.330.2041710.1543011X-RAY DIFFRACTION99.34
4.33-38.210.20821260.16113074X-RAY DIFFRACTION99.66
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)
16.01343641884-0.3246691252883.50944855952.665416955681.869009529463.63674732580.05051404523270.6272315472850.675865522995-0.3672842792930.161352946604-0.0808904868245-1.516415701371.51415444621-0.2855722535480.489689894138-0.08352529834250.05665781638190.3644457044840.004516759356670.3057139779418.746701396326.661715507631.6843139796
23.080391827860.9613396592273.368955772524.90433779918-0.1591417748324.57847300631-0.0849623935338-0.3243844531520.1393083438830.1222630738870.1703745757220.432429836629-0.516531268688-0.586817627904-0.1349964484380.2913223764580.05711837721790.000303636005590.2503379682440.02069687233010.2342751740047.9227213826127.076880450441.634371323
32.67767173878-2.50495183886-1.52110754187.48136772053-0.1834208479332.2997041706-0.271680864186-0.225406511933-0.1816816082760.6534186620.4381668209330.332605515049-0.0201218043721-0.131283913187-0.1934097228230.2610540651260.005548379699850.01619379201330.2307096725990.02988342128140.24005105517511.222531801919.641866352845.8050621447
43.053487891662.46865908356-0.3239984494517.07287874942-3.476905224072.367450632910.17515405784-0.6389761917510.1012486388130.81301523467-0.125510954631-0.379880332838-0.07996929256980.816623885272-0.02946893359280.379303436958-0.00531911844850.046456245330.575266591016-0.08818143766710.33360775220419.472554895724.395538048547.56608462
55.332505653793.00922923475-4.502460118917.72666441822-5.575007317495.32962158469-0.130481474026-1.124316864580.8289250006590.808011132916-0.0445653029483-0.587631913859-1.211522182261.002719803170.2971153345230.486441005287-0.0794719950495-0.003811585298050.300248773659-0.00478067645130.37023883885218.50960685834.937694098339.2692599114
66.49196593379-0.836788310997-2.259669502084.901099066482.016871446082.044209908780.114161222323-0.8864447783650.6132824006040.373461873074-0.163605695787-0.0811620674961-0.455268930616-0.08160947939080.04769943515140.5805462924510.00467955892710.01565883948450.382356407083-0.05452256355630.3659074922929.9954794736537.455104505847.7558898564
75.75892686001-1.14009085903-0.5477506180513.713881305063.483883105253.300604520930.03294306272220.8580189124590.675016326485-0.62710558130.0567368177301-0.0861516735738-1.93701286143-0.16890177134-0.1674534845970.5612404944550.0400613625567-0.03120790258110.2915721533160.06869767337030.2920768642278.2968371285832.315107135130.1774631918
85.268547420050.215573631513-0.6414090973073.19025692770.4674159412293.217896705180.106837884052-0.208839370701-0.2854457565340.107827694175-0.1005508976230.02670382833610.0181711085921-0.3531096583290.006617437091730.178994739775-0.0070464894619-0.04915929325430.3273401558410.02238030846260.2354272609121.560843571314.829578063825.1271208483
92.810833178850.331877411651-3.085604650713.654104097691.999188872984.93535492635-0.305194493638-1.19658951791-0.740120669090.656550549353-0.525211306441-0.2192880255420.6019537582630.5210724643180.8279594477220.292716435039-0.006147405470690.04571586727610.3940364797990.07013045989140.27161978937819.657523050814.083573208634.1286542171
106.36733414436-0.2707183362610.1753637068446.81269844211-1.162072029871.273240686450.1142909845240.259439290327-0.211713195348-0.394285722676-0.1111864485180.61438871751-0.103584228468-0.681002070704-0.06401209728240.1981187180880.00654280873411-0.0239745210310.2623664847390.01069886450590.25299621795717.022700830611.765221672920.3260138234
111.14586719843-1.59814706908-1.035481381297.204437497212.620943383883.007860673740.2947254812350.1153712985110.0143818498758-0.787415416474-0.1856460337720.11774945204-0.598834113951-0.0685488449354-0.1203703864960.277232920266-0.01645401225730.00382837341740.264484219898-0.00389552279120.2113116762421.589584923119.448541009417.3060605754
122.860187103550.5863049306290.1963288414782.07747492335-1.48351520574.553069439580.05400438158240.1489896103130.180055619606-0.0994807599391-0.392466444482-0.507136939313-0.3305931543740.3628646198250.2567881718430.223503729082-0.0315381173536-0.04381628784720.367686434867-0.02191667305180.30818313379129.14129729916.827929301822.5649059146
136.3250746525-2.51654435345-3.2044806285.69325432396-0.5839334497092.39292762606-0.194735519118-0.189844458482-0.497473104033-0.1503259957220.0920860705273-0.4059473384570.4771069062780.8151470102110.1282726201070.251580588290.0311249962128-0.02329859062930.3033654462050.04321492076110.40037816372523.89965834934.396870733426.9153874895
142.42721161499-0.218596348493-2.576716178270.878026756817-0.7415654903053.832535068791.059426380210.7324805107690.20809361738-0.563014943172-0.294124010546-0.624082949895-0.7312975445510.901824449116-0.656698571350.9678870001430.00632976065060.3102353910551.19180318578-0.3679566171971.1447725225331.41457919172.3434482645711.8492883488
156.38464306489-0.134299199085-1.229620951465.413288612970.1495779049855.58061409808-0.297003566272-0.600603875072-0.7038567596190.2060440092840.0942109406456-0.2229030023570.7684231321850.5802882195480.1978880663090.1905364632940.00520359733983-0.06963441646060.2319867623440.0277747745120.31839781379816.15526280485.762525209125.4519572556
162.521368099811.204716735081.598573061593.718430239270.8491969989775.328370797540.1264258118230.2534235301470.162293106059-0.185995258746-0.0154535486750.147432075228-0.304226149735-0.36249576765-0.1096049020070.2075966062010.0659819634768-0.002489819779890.3736829595440.01720456986350.2778606020010.27599007969321.049736547327.1471304696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 11:19)
2X-RAY DIFFRACTION2(chain A and resid 20:34)
3X-RAY DIFFRACTION3(chain A and resid 35:45)
4X-RAY DIFFRACTION4(chain A and resid 46:56)
5X-RAY DIFFRACTION5(chain A and resid 57:63)
6X-RAY DIFFRACTION6(chain A and resid 64:79)
7X-RAY DIFFRACTION7(chain A and resid 80:90)
8X-RAY DIFFRACTION8(chain A and resid 91:120)
9X-RAY DIFFRACTION9(chain B and resid 11:19)
10X-RAY DIFFRACTION10(chain B and resid 20:32)
11X-RAY DIFFRACTION11(chain B and resid 33:45)
12X-RAY DIFFRACTION12(chain B and resid 46:58)
13X-RAY DIFFRACTION13(chain B and resid 59:69)
14X-RAY DIFFRACTION14(chain B and resid 70:74)
15X-RAY DIFFRACTION15(chain B and resid 75:90)
16X-RAY DIFFRACTION16(chain B and resid 91:120)

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