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- PDB-9ca5: Rns pocket mutant - H20A -

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Basic information

Entry
Database: PDB / ID: 9ca5
TitleRns pocket mutant - H20A
ComponentsAraC-family, transcriptional regulator Rns
KeywordsDNA BINDING PROTEIN / Mutation / DNA Binding / AraC Family
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily
Similarity search - Domain/homology
AraC-family, transcriptional regulator Rns
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTolbert, J.D. / Midget, C.R. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI168157 United States
Citation
Journal: To Be Published
Title: Structure of Regulatory protein Rns
Authors: Tolbert, J.F. / Talbot, K.M. / Midgett, C.R. / Munson, G.P. / Kull, F.J.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AraC-family, transcriptional regulator Rns
B: AraC-family, transcriptional regulator Rns


Theoretical massNumber of molelcules
Total (without water)61,6062
Polymers61,6062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-10 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.730, 97.930, 136.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 93 or resid 103...
d_2ens_1(chain "B" and (resid 9 through 124 or resid 126...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSGLYGLYAA9 - 939 - 93
d_12ARGARGASNASNAA103 - 124103 - 124
d_13ASNASNSERSERAA126 - 127126 - 127
d_14ASNASNGLUGLUAA130 - 171130 - 171
d_15ASPASPARGARGAA173 - 176173 - 176
d_16TRPTRPPHEPHEAA178 - 262178 - 262
d_21LYSLYSASNASNBB9 - 1249 - 124
d_22ASNASNSERSERBB126 - 127126 - 127
d_23ASNASNGLUGLUBB130 - 171130 - 171
d_24ASPASPARGARGBB173 - 176173 - 176
d_25TRPTRPPHEPHEBB178 - 262178 - 262

NCS oper: (Code: givenMatrix: (-0.999666916069, -0.0257700862902, -0.00139984635365), (-0.0257320729036, 0.999415308827, -0.0225144599249), (0.00197922745089, -0.0224709397717, -0.999745537387)Vector: ...NCS oper: (Code: given
Matrix: (-0.999666916069, -0.0257700862902, -0.00139984635365), (-0.0257320729036, 0.999415308827, -0.0225144599249), (0.00197922745089, -0.0224709397717, -0.999745537387)
Vector: -0.0803531543984, 0.189633716683, 18.1995524988)

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Components

#1: Protein AraC-family, transcriptional regulator Rns


Mass: 30802.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7ZGQ6
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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1:1 v/v DMSO, 0.1 M succinnic acid, 14% PEG 3350, 0.03 M glycyl-glycyl-gylcine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979351 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979351 Å / Relative weight: 1
ReflectionResolution: 2.9→46.1 Å / Num. obs: 13705 / % possible obs: 92.34 % / Redundancy: 3.6 % / Biso Wilson estimate: 87.44 Å2 / CC1/2: 0.986 / CC star: 0.996 / Net I/σ(I): 3.08
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 1448 / CC1/2: 0.0739 / CC star: 0.371

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.1 Å / SU ML: 0.5663 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.26
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3149 1372 10.02 %
Rwork0.2641 12336 -
obs0.2694 13705 92.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.08 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 0 0 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634083
X-RAY DIFFRACTIONf_angle_d0.74935479
X-RAY DIFFRACTIONf_chiral_restr0.0478635
X-RAY DIFFRACTIONf_plane_restr0.0078677
X-RAY DIFFRACTIONf_dihedral_angle_d15.42491559
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.753985605881 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.4561460.40991372X-RAY DIFFRACTION99.31
3-3.120.38191440.37231290X-RAY DIFFRACTION99.38
3.12-3.270.38381460.34341305X-RAY DIFFRACTION99.93
3.27-3.410.38811250.31561136X-RAY DIFFRACTION99.37
3.47-3.640.37891150.29121040X-RAY DIFFRACTION99.14
3.7-3.940.3599910.2917815X-RAY DIFFRACTION75.88
3.94-4.330.33141490.24521332X-RAY DIFFRACTION99.66
4.33-4.960.30351480.20661331X-RAY DIFFRACTION99.2
4.96-6.240.29891510.27521353X-RAY DIFFRACTION99.41
6.25-46.10.24491610.23551429X-RAY DIFFRACTION99.19
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)
14.19609618462-1.00363975888-4.407635290292.591866006392.613440240997.458755762850.06410852623760.0850775282818-0.4024028906320.486289494554-0.09783089903430.143988645605-0.167138223638-0.1972757887110.06670289175760.735115767161-0.0604082437381-0.07043044434120.648119467950.09082967994340.79522450038611.6004480288-7.90334351676-4.1054607499
24.81326563494-1.11917005229-2.903346381227.60516962833-4.982095259157.062041663350.45191725511-0.06792341774680.6245924242860.74192167115-1.09481767546-0.666006632174-0.5553781624740.3826880473340.9470637818770.620203206162-0.161736962002-0.03223626949040.859386411921-0.08528159341950.73271492035814.07014703212.6959742857-11.9334922667
36.20516316331-4.612059491681.155297094484.038341942490.7726748234464.43192991287-0.1615628077560.312281768674-0.410021756887-0.109306425419-0.02314061175060.36286504905-0.4858444497020.528092448127-0.0188029199340.599741761886-0.02237067089420.07077873995050.799182283180.03657137561290.67372851664911.5594810561-2.40469121074-26.547451097
42.45106157616-0.1881766913580.2171521062141.30402268455-0.2687220308740.6901719591950.1445035847210.393057289425-0.184598759007-0.152529771535-0.2389944269590.002980813402880.0496443243239-0.06847207293010.05658280311070.917922076283-0.00450554901618-0.05428259736650.730283177618-0.04475133990460.761319203629-11.6275292266-2.8866346491524.4156351709
50.4600692411020.257328994028-0.4071082184437.82884868122-2.16885693450.7776954493720.185395369925-0.1502140231210.001899070364910.107778922095-0.09557273713350.9490256671460.14590068036-0.242322954009-0.05077447788830.5040611968710.000315203101073-0.03841217656180.812777489584-0.02920971013390.778426304896-13.51385428111.5545197546242.3694349475
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 143 )AA9 - 1431 - 128
22chain 'A' and (resid 144 through 204 )AA144 - 204129 - 189
33chain 'A' and (resid 205 through 262 )AA205 - 262190 - 247
44chain 'B' and (resid 9 through 190 )BB9 - 1901 - 173
55chain 'B' and (resid 191 through 263 )BB191 - 263174 - 246

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