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

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Basic information

Entry
Database: PDB / ID: 9bul
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


small molecule binding / 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: 2.1 Å
AuthorsGlasfeld, A. / Cheng, D.W.C. / Li, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of NiaR from Thermotoga maritima bound to nicotinic acid
Authors: Glasfeld, A. / Cheng, D.W.C. / Li, Y.
History
DepositionMay 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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-43 kcal/mol
Surface area18870 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 (E. coli) / 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: isolated from a natural source / 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

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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 / pH: 7.5
Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10% (w/v) PEG 3350, 1 mM 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: 2.1→35.33 Å / Num. obs: 15968 / % possible obs: 99.86 % / Redundancy: 10 % / Biso Wilson estimate: 64.88 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.01368 / Net I/σ(I): 32.28
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.67 / Num. unique obs: 1590 / CC1/2: 0.639 / CC star: 0.883 / Rpim(I) all: 0.6771 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.33 Å / SU ML: 0.3663 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.1387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 755 4.73 %
Rwork0.2248 15202 -
obs0.227 15957 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 18 9 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491353
X-RAY DIFFRACTIONf_angle_d0.73511822
X-RAY DIFFRACTIONf_chiral_restr0.0491215
X-RAY DIFFRACTIONf_plane_restr0.0044234
X-RAY DIFFRACTIONf_dihedral_angle_d16.1027530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.39931160.35023028X-RAY DIFFRACTION99.87
2.26-2.490.36931510.35693000X-RAY DIFFRACTION99.9
2.49-2.850.36911330.35733024X-RAY DIFFRACTION99.97
2.85-3.590.33911860.29123012X-RAY DIFFRACTION100
3.59-35.330.21821690.16743138X-RAY DIFFRACTION99.82
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)
17.45497292613-1.36258047442-0.2414038400965.73098592956-6.461485178187.59461589096-0.697487742992-0.483836209048-0.07497480217510.4822580065990.0410853904498-0.721417994293-0.1732208489371.036432319060.5846533827430.7073686105140.03931736517880.020790797150.5107043142550.04772808670020.570462856237-23.244-20.26111.169
27.93405317274-2.56743894083-1.953393966713.37304898224.465329161746.877238131850.603110857949-0.5808819348730.328713030723-0.672640610318-0.11486364334-1.81469418043-0.6843598689970.712938509883-0.2003641654910.789702614322-0.02218072503280.04987212991550.8163536989470.09242063761440.855986656181-14.071-18.8395.185
39.38312484146-1.407445272641.169892885856.75809534058-0.4492412829266.086402958130.321084058191-0.752661210321-0.5246910115911.09327037338-0.199138280772-0.5631246421020.478898889755-0.0957407689443-0.08057203826850.843600474612-0.273596592881-0.248976053220.6209797616370.05521946218210.5984952851513.013-33.486.622
47.724636721714.25724945333-6.230679589962.3070458507-3.34094458835.580833529660.5502935406860.6875347528250.4920144811340.2102782257250.497449685907-0.0629534492015-0.543679171491-0.420035502068-0.7254233671610.653439071981-0.263479311247-0.1467432416870.6281573100690.04865542868150.66568454791219.444-25.619-6.633
59.75912402263-2.430944713320.8687077672717.37310654222-0.8480770539425.727865561130.643653972051-0.569847591555-1.694897277030.635495800898-0.3620001003730.3669418690691.20611520351-0.63944287077-0.1656107365040.741261958327-0.359650904022-0.2443904008140.5542762154890.09429175553970.671462741756.118-38.484-1.373
69.22065553765-2.208580049382.895054650136.175906508650.2242460048968.48518053238-0.0426489220374-1.168035477530.5578164788671.99199524538-0.115430457558-1.04675705680.03360741082560.1902173996850.02062455096330.901167429999-0.293919051061-0.3557286327260.7327492579840.07599393903770.73121257376916.42-31.0547.127
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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