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- PDB-5m7p: Crystal structure of NtrX from Brucella abortus in complex with A... -

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Basic information

Entry
Database: PDB / ID: 5m7p
TitleCrystal structure of NtrX from Brucella abortus in complex with ADP processed with the CrystalDirect automated mounting and cryo-cooling technology
ComponentsNitrogen assimilation regulatory protein
KeywordsSIGNALING PROTEIN / CRYSTALDIRECT / BRUCELLOSIS / TWO-COMPONENT SYSTEM
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Response regulator receiver domain ...Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nitrogen assimilation regulatory protein
Similarity search - Component
Biological speciesBrucella abortus str. 2308 A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.36 Å
AuthorsCornaciu, I. / Fernandez, I. / Hoffmann, G. / Carrica, M.C. / Goldbaum, F.A. / Marquez, J.A.
Funding support Argentina, France, 3items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y TecnologicaPICT-2013-1629 Argentina
BioStruct-X283570 France
iNEXT653706 France
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Three-Dimensional Structure of Full-Length NtrX, an Unusual Member of the NtrC Family of Response Regulators.
Authors: Fernandez, I. / Cornaciu, I. / Carrica, M.D. / Uchikawa, E. / Hoffmann, G. / Sieira, R. / Marquez, J.A. / Goldbaum, F.A.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Data collection
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Nitrogen assimilation regulatory protein
B: Nitrogen assimilation regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4646
Polymers100,5612
Non-polymers9034
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-63 kcal/mol
Surface area36760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.979, 190.840, 111.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Nitrogen assimilation regulatory protein


Mass: 50280.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The missing residues could not be modeled in the partial electron density.
Source: (gene. exp.) Brucella abortus str. 2308 A (bacteria)
Gene: BAAA_2000042 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: C4IRH0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.36 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.36→29.87 Å / Num. obs: 51562 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 53.93 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.034 / Rrim(I) all: 0.077 / Net I/σ(I): 14.7
Reflection shellResolution: 2.36→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2 / CC1/2: 0.712 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.36→29.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2517 4.88 %RANDOM
Rwork0.199 ---
obs0.201 51541 99.7 %-
Displacement parametersBiso mean: 54.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.9667 Å20 Å20 Å2
2--9.3091 Å20 Å2
3----13.2758 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.36→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6693 0 56 293 7042
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096841HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.079271HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2447SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes171HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1030HARMONIC5
X-RAY DIFFRACTIONt_it6841HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion16.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion935SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8117SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 178 4.8 %
Rwork0.249 3530 -
all0.251 3708 -
obs--98.61 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
139.528130.583116.0408
228.430124.38157.6516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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