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- PDB-4d6y: Crystal structure of the receiver domain of NtrX from Brucella ab... -

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Basic information

Entry
Database: PDB / ID: 4d6y
TitleCrystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / 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: 1.7 Å
AuthorsOtero, L.H. / Fernandez, I. / Carrica, M.C. / Klinke, S. / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8466
Polymers32,6652
Non-polymers1814
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.395, 39.343, 52.961
Angle α, β, γ (deg.)97.30, 96.97, 89.97
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 16332.590 Da / Num. of mol.: 2 / 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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.91 Å3/Da / Density % sol: 35.64 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 22% PEG 400; 0.1 M MES, PH 6.9; 5 MM MGCL2, 5 MM BEF3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→39.02 Å / Num. obs: 25833 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 22.05 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.4 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D6X

4d6x


Resolution: 1.7→19.99 Å / Cor.coef. Fo:Fc: 0.9398 / Cor.coef. Fo:Fc free: 0.9367 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1279 4.95 %RANDOM
Rwork0.1836 ---
obs0.1847 25818 97.25 %-
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.2574 Å21.4411 Å20.4634 Å2
2---2.1312 Å2-1.1697 Å2
3----2.1262 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 10 106 1996
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011912HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022588HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d912SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes276HARMONIC5
X-RAY DIFFRACTIONt_it1912HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion2.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion258SEMIHARMONIC5
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_contact2407SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.77 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2718 137 4.81 %
Rwork0.1937 2714 -
all0.1973 2851 -
obs--97.25 %
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)
13.9833-0.15350.94951.7037-0.05922.1369-0.2562-0.32620.34140.09210.13390.009-0.1576-0.04420.1223-0.05660.0295-0.0137-0.0653-0.0031-0.051-51.168626.299618.8054
24.0315-0.1995-1.00632.01930.08162.2132-0.20320.2681-0.334-0.07850.10970.050.1146-0.03390.0935-0.0763-0.02980.0319-0.07930.0031-0.038-50.99788.811-6.2422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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