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- PDB-4d6x: Crystal structure of the receiver domain of NtrX from Brucella abortus -

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Basic information

Entry
Database: PDB / ID: 4d6x
TitleCrystal structure of the receiver domain of NtrX from Brucella abortus
ComponentsBACTERIAL REGULATORY, FIS FAMILY PROTEIN
KeywordsSIGNALING PROTEIN / BRUCELLOSIS / TWO-COMPONENT SYSTEM / RESPONSE REGULATOR / REC DOMAIN / MICROAEROBISIS
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 / Response regulator / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / CbxX/CfqX superfamily:Chaperonin clpA/B:Response regulator receiver:Sigma-54 factor interaction domain:Helix-turn-helix, Fis
Similarity search - Component
Biological speciesBRUCELLA ABORTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKlinke, S. / Fernandez, I. / Carrica, M.C. / Otero, L.H. / Goldbaum, F.A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Snapshots of Conformational Changes Shed Light Into the Ntrx Receiver Domain Signal Transduction Mechanism
Authors: Fernandez, I. / Otero, L.H. / Klinke, S. / Carrica, M.C. / Goldbaum, F.A.
History
DepositionNov 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
B: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
C: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
D: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5387
Polymers65,3304
Non-polymers2073
Water1,49583
1
A: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4713
Polymers16,3331
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BACTERIAL REGULATORY, FIS FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4022
Polymers16,3331
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BACTERIAL REGULATORY, FIS FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,3331
Polymers16,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BACTERIAL REGULATORY, FIS FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,3331
Polymers16,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 110.940, 119.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
BACTERIAL REGULATORY, FIS FAMILY PROTEIN / NTRX


Mass: 16332.590 Da / Num. of mol.: 4 / Fragment: RECEIVER DOMAIN, RESIDUES 1-126
Source method: isolated from a genetically manipulated source
Details: THE GENE SEQUENCE ENCODING THE RECEIVER DOMAIN C-TERMINAL REGION (RESIDUES 127-136) WAS OMITTED FROM THE FINAL CONSTRUCT DUE TO POTENTIAL CLASHES INTO THE CRYSTAL PACKING
Source: (gene. exp.) BRUCELLA ABORTUS (bacteria) / Strain: BRUCELLA MELITENSIS BIOVAR ABORTUS 2308 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q2YPW6
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.96 Å3/Da / Density % sol: 37.33 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 27% PEG 550 MME; 0.15 M MALIC ACID, PH 7.0; 0.1 M IMIDAZOLE, PH 6.9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.11→40.64 Å / Num. obs: 30141 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 5.11 % / Biso Wilson estimate: 57.41 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.63
Reflection shellResolution: 2.11→2.24 Å / Redundancy: 5.28 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.98 / % possible all: 98.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L5Z

1l5z


Resolution: 2.11→40.64 Å / Cor.coef. Fo:Fc: 0.9523 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 1507 5 %RANDOM
Rwork0.2134 ---
obs0.2137 30132 98.82 %-
Displacement parametersBiso mean: 74.48 Å2
Baniso -1Baniso -2Baniso -3
1--14.2838 Å20 Å20 Å2
2--9.264 Å20 Å2
3---5.0198 Å2
Refine analyzeLuzzati coordinate error obs: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2.11→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 15 83 3810
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013779HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085119HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1794SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it3779HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion508SEMIHARMONIC5
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_contact4511SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.18 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2257 144 5.01 %
Rwork0.2369 2732 -
all0.2363 2876 -
obs--98.82 %
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)
13.17551.76660.22298.30290.75571.634-0.0968-0.0036-0.5442-0.22-0.01190.00750.5442-0.23450.10870.1628-0.0459-0.1145-0.2963-0.0439-0.17024.656319.12219.9659
21.25480.5715-0.07732.4113-0.92068.2844-0.0415-0.18050.27920.54420.04530.0628-0.54420.4408-0.00380.06890.041-0.088-0.1973-0.0525-0.159711.912640.680138.0896
35.3983-1.66892.21328.3155-1.92844.6578-0.2587-0.45960.04720.52440.2081-0.0077-0.5442-0.36940.0506-0.04880.0334-0.0498-0.1945-0.0091-0.230914.435614.918551.4707
42.3658-0.0004-0.01645.03361.93163.67690.1926-0.2717-0.02740.4173-0.0243-0.02550.20320.1564-0.1684-0.1157-0.0348-0.0329-0.07410.0304-0.0836-7.3242-9.955550.233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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