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- PDB-9ebr: The structure of NiaR from Thermotoga maritima bound to nicotinic acid -

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Basic information

Entry
Database: PDB / ID: 9ebr
TitleThe structure of NiaR from Thermotoga maritima bound to nicotinic acid
ComponentsProbable transcription repressor NiaR
KeywordsDNA BINDING PROTEIN / Corepressor / regulatory protein / metalloprotein
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
3H domain / Transcription repressor NadR / 3H domain superfamily / 3H domain / Helix-turn-helix, type 11 / HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINIC ACID / PROLINE / Probable transcription repressor NiaR
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGlasfeld, A. / Cheng, D.W.C. / Li, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Inorg.Chem. / Year: 2025
Title: The activation of the metal-containing regulatory protein NiaR from Thermotoga maritima by its effector, nicotinic acid.
Authors: Cheng, W.C.D. / Li, Y. / Nakashima, M. / Moenne-Loccoz, P. / Rush, K.W. / Glasfeld, A.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
SupersessionJan 22, 2025ID: 9BUL
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable transcription repressor NiaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8784
Polymers19,5841
Non-polymers2943
Water1629
1
A: Probable transcription repressor NiaR
hetero molecules

A: Probable transcription repressor NiaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7568
Polymers39,1682
Non-polymers5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2610 Å2
ΔGint-40 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.243, 83.243, 66.838
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Probable transcription repressor NiaR


Mass: 19583.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: niaR, TM_1602 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1T8
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M L-PROLINE, 0.1 M HEPES PH 7.5, 10% (W/V) PEG 3350, .001 M NICOTINIC ACID

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→35.33 Å / Num. obs: 12235 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 65.89 Å2 / CC1/2: 1 / Rpim(I) all: 0.014 / Rrim(I) all: 0.032 / Net I/σ(I): 35.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1190 / CC1/2: 0.935 / Rpim(I) all: 0.243 / Rrim(I) all: 0.559 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35.33 Å / SU ML: 0.3279 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.4137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 614 5.03 %
Rwork0.2174 11591 -
obs0.2197 12205 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 18 9 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791353
X-RAY DIFFRACTIONf_angle_d0.97091822
X-RAY DIFFRACTIONf_chiral_restr0.0517215
X-RAY DIFFRACTIONf_plane_restr0.0087234
X-RAY DIFFRACTIONf_dihedral_angle_d16.5491530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.40721450.34632859X-RAY DIFFRACTION99.87
2.53-2.90.30551400.27562874X-RAY DIFFRACTION99.97
2.9-3.650.32061670.29362865X-RAY DIFFRACTION100
3.65-35.330.21971620.17042993X-RAY DIFFRACTION99.81
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)
19.58252833819-2.655543228060.01969867311178.24625960367-6.788151819289.09722005636-0.787054542921-0.42781309905-0.2220292244110.4050281577240.14233894382-0.526516848543-0.3372858538230.9195245410430.6646185735380.6975563250260.008561857647080.0227147832380.51370013080.04742500774320.521511627167-23.257-20.26911.175
29.07449157586-3.54943889136-3.641010460699.877515289346.175898242048.989625162460.395503118702-0.7021993793590.856478366143-0.789428007586-0.098985339503-1.67937040051-1.068616579170.825706192055-0.3992084794550.767077766199-0.04882759016020.04970096146570.8698010286120.1089368580550.853013484516-14.064-18.8415.198
36.45667947281-0.4820067557221.741990747886.32415216176-0.3560002657118.08278796030.347671885274-0.994579459764-0.5726316774841.02216576707-0.0967016492948-0.5122544919830.447495664751-0.098549606826-0.1047317199630.872529441525-0.27403475044-0.2834497147050.6123756135470.07634565744130.69960449066713.013-33.4726.624
49.067490419835.03251034253-7.55153662472.71613524488-3.989720734417.523281838240.6530515797550.5631112899060.4035350312910.1741861010860.39214376433-0.213276862639-0.616085612253-0.465604224204-0.9191323764860.651355004702-0.254498859613-0.1655946284550.5946411327070.04895819000790.68118427051719.446-25.603-6.594
52.44239438908-1.777425523940.9015353052386.93277583242-1.941932504276.699098628290.511602940723-0.351181614783-1.305006169690.247115965958-0.3171530186720.2708689902811.19412789066-0.769346989068-0.2208851710910.822551629252-0.345207110007-0.2474050878970.691225264070.08708356593980.797842527966.121-38.491-1.368
69.54075309562-1.742155395493.931532959515.676516836810.07345337301927.81439013822-0.081599527531-1.169475287220.5480399245071.95812852967-0.16715734551-0.965281379760.1897651991750.01430256657180.05083127202770.926752644062-0.289488209537-0.3454067159370.7973184259640.06570430907070.77771455588316.417-31.0527.135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:48 )A6 - 48
2X-RAY DIFFRACTION2( CHAIN A AND RESID 49:68 )A49 - 68
3X-RAY DIFFRACTION3( CHAIN A AND RESID 69:98 )A69 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:112 )A99 - 112
5X-RAY DIFFRACTION5( CHAIN A AND RESID 113:133 )A113 - 133
6X-RAY DIFFRACTION6( CHAIN A AND RESID 134:173 )A134 - 173

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