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- PDB-1ew0: CRYSTAL STRUCTURE ANALYSIS OF THE SENSOR DOMAIN OF RMFIXL(FERROUS... -

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Basic information

Entry
Database: PDB / ID: 1ew0
TitleCRYSTAL STRUCTURE ANALYSIS OF THE SENSOR DOMAIN OF RMFIXL(FERROUS FORM)
ComponentsFIXL
KeywordsTRANSFERASE / OXYGEN SENSOR / HEME PROTEIN / HISTIDINE KINASE / RHIZOBIUM MELILOTI
Function / homology
Function and homology information


nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) 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. ...PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) 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 speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsMiyatake, H. / Mukai, M. / Park, S.-Y. / Adachi, S. / Tamura, K. / Nakamura, H. / Nakamura, K. / Tsuchiya, T. / Iizuka, T. / Shiro, Y.
Citation
Journal: J.MOL.BIOL. / Year: 2000
Title: Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies
Authors: Miyatake, H. / Mukai, M. / Park, S.-Y. / Adachi, S. / Tamura, K. / Nakamura, H. / Nakamura, K. / Tsuchiya, T. / Iizuka, T. / Shiro, Y.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999
Title: Dynamic light-scattering and preliminary crystallographic studies of the sensor domain of the haem-based oxygen sensor FixL from Rhizobium meliloti.
Authors: Miyatake, H. / Kanai, M. / Adachi, S. / Nakamura, H. / Tamura, K. / Tanida, H. / Tsuchiya, T. / Iizuka, T. / Shiro, Y.
#2: Journal: J.Biol.Chem. / Year: 1999
Title: Iron coordination structure of oxygen sensor FixL characterized by Fe K-edge EXAFS and resonance Raman spectroscopy
Authors: Miyatake, H. / Mukai, M. / Adachi, S. / Nakamura, H. / Tamura, K. / Iizuka, T. / Shiro, Y. / Strange, R.W. / Hasnain, S.S.
History
DepositionApr 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: FIXL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1392
Polymers14,5221
Non-polymers6161
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.300, 37.040, 53.450
Angle α, β, γ (deg.)90.00, 115.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FIXL


Mass: 14522.385 Da / Num. of mol.: 1 / Fragment: SENSOR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Plasmid: PET-14B / Production host: Escherichia coli (E. coli)
References: UniProt: P10955, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#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.: 68 / 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: 1.86 Å3/Da / Density % sol: 33.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, acetic acid/NaOH, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMprotein1drop
2100 mMsodium acetate1reservoir
3200 mMammonium acetate1reservoir
440 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. all: 165005 / Num. obs: 33489 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.93 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.7
Reflection shellResolution: 1.2→1.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.278 / Num. unique all: 4730 / % possible all: 84.4
Reflection
*PLUS
Num. measured all: 165005

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 1.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 982 -RANDOM
Rwork0.205 ---
all0.205 19646 --
obs0.205 18664 92.1 %-
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 43 68 1130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.527
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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