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- PDB-2cmn: A Proximal Arginine Residue in the Switching Mechanism of the Fix... -

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Basic information

Entry
Database: PDB / ID: 2cmn
TitleA Proximal Arginine Residue in the Switching Mechanism of the FixL Oxygen Sensor
ComponentsSENSOR PROTEIN FIXL
KeywordsTRANSFERASE / SENSORY TRANSDUCTION / TWO- COMPONENT SYSTEM / TRANSMEMBRANE / INNER MEMBRANE / NITROGEN FIXATION
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding
Similarity search - Function
PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal ...PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Sensor protein FixL
Similarity search - Component
Biological speciesBRADYRHIZOBIUM JAPONICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGilles-Gonzalez, M.-A. / Caceres, A.I. / Silva Sousa, E.H. / Tomchick, D.R. / Brautigam, C.A. / Gonzalez, C. / Machius, M.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: A Proximal Arginine R206 Participates in Switching of the Bradyrhizobium Japonicum Fixl Oxygen Sensor
Authors: Gilles-Gonzalez, M.-A. / Caceres, A.I. / Silva Sousa, E.H. / Tomchick, D.R. / Brautigam, C.A. / Gonzalez, C. / Machius, M.
#1: Journal: Mgg,Mol.Gen.Genet. / Year: 1991
Title: The Regulatory Status of the Fixl- and Fixj-Like Genes in Bradyrhizobium Japonicum May be Different from that in Rhizobium Meliloti
Authors: Anthamatten, D. / Hennecke, H.
#2: Journal: Biochemistry / Year: 2003
Title: A Distal Arginine in Oxygen-Sensing Heme-Pas Domains is Essential to Ligand Binding, Signal Transduction, and Structure.
Authors: Dunham, C.M. / Dioum, E.M. / Tuckerman, J.R. / Gonzalez, G. / Scott, W.G. / Gilles-Gonzalez, M.A.
History
DepositionMay 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 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_conn
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SENSOR PROTEIN FIXL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3192
Polymers14,7031
Non-polymers6161
Water59433
1
A: SENSOR PROTEIN FIXL
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)91,91412
Polymers88,2156
Non-polymers3,6996
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_546y+1/3,x-1/3,-z+5/31
crystal symmetry operation17_556x-y+1/3,-y+2/3,-z+5/31
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation18_656-x+4/3,-x+y+2/3,-z+5/31
Buried area15070 Å2
ΔGint-179.7 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.117, 127.117, 58.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein SENSOR PROTEIN FIXL / / PROTEIN HISTIDINE KINASE FIXL


Mass: 14702.545 Da / Num. of mol.: 1 / Fragment: HEME-PAS DOMAIN, RESIDUES 141-270 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: P23222, histidine kinase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 206 TO ALA FUNCTION:TAKES PART IN TRANSCRIPTIONAL ACTIVATION OF ...ENGINEERED RESIDUE IN CHAIN A, ARG 206 TO ALA FUNCTION:TAKES PART IN TRANSCRIPTIONAL ACTIVATION OF THE FIXK GENE INVOLVED IN NITROGEN FIXATIN.FIXL ALSO DISPLAYS A KINASE ACTIVITY PHOSPHORYLATING FIXJ.IT CAN ALSO ACT AS A PUTATIVE OXYGEN SENSOR.

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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: 3.25 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: CRYSTALS OF THE MET-R206A BJFIXLH MUTANT WERE OBTAINED AT 4 DEGREES C VIA THE HANGING-DROP VAPOR-DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (0.6-1.2 MM IN 5.0 MM TRIS-HCL, PH 8.0) ...Details: CRYSTALS OF THE MET-R206A BJFIXLH MUTANT WERE OBTAINED AT 4 DEGREES C VIA THE HANGING-DROP VAPOR-DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (0.6-1.2 MM IN 5.0 MM TRIS-HCL, PH 8.0) AND WELL SOLUTION (50 MM HEPES, 4.5 M NACL, 5% (V/) 2-METHYL-2,4-PENTANEDIOL, PH 7.5) AND INCUBATING THE DROP OVER 0.7 ML OF WELL SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978
DetectorType: CUSTOM / Detector: CCD / Date: Oct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→27.07 Å / Num. obs: 8187 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LSW

1lsw


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.713 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 611 7.5 %RANDOM
Rwork0.195 ---
obs0.197 7565 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 43 33 1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6932.081357
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0065116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.823.33348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97515159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.68159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02887
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2392
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2651
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7211.5599
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0932933
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.693451
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4764.5422
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 48
Rwork0.28 537
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)
14.17631.8981-0.02734.38730.933.40280.2115-0.1624-0.0372-0.1225-0.1325-0.1163-0.0817-0.1763-0.0789-0.02760.06130.04-0.15430.0433-0.152550.878758.657536.6512
233.2872-21.4981-7.737419.24074.039313.7070.34950.52020.0128-0.4408-0.41940.3119-0.25080.48180.0699-0.2265-0.0346-0.065-0.09020.081-0.001469.498440.64329.617
31.48830.3002-2.88886.4303-6.396510.9137-0.09960.3034-0.0693-0.1656-0.41950.20260.2323-0.15270.51910.11450.05160.0041-0.02650.0355-0.066247.28554.915233.6047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A154 - 256
2X-RAY DIFFRACTION2A257 - 270
3X-RAY DIFFRACTION3A1271

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