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- PDB-1d06: STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN... -

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Basic information

Entry
Database: PDB / ID: 1d06
TitleSTRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION
Componentsnitrogen fixation regulatory protein fixL
KeywordsSIGNALING PROTEIN / OXYGEN SENSOR / HISTIDINE KINASE / PAS / HIGH-RESOLUTION / TWO-COMPONENT SYSTEM
Function / homology
Function and homology information


nitrogen fixation / phosphorelay sensor kinase activity / histidine kinase / 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 / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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 / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / 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.
CitationJournal: 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.
History
DepositionSep 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nitrogen fixation regulatory protein fixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1392
Polymers14,5221
Non-polymers6161
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: nitrogen fixation regulatory protein fixL
hetero molecules

A: nitrogen fixation regulatory protein fixL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2784
Polymers29,0452
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5280 Å2
ΔGint-67 kcal/mol
Surface area12170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.600, 37.150, 53.990
Angle α, β, γ (deg.)90.00, 115.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein nitrogen fixation regulatory protein fixL


Mass: 14522.385 Da / Num. of mol.: 1 / Mutation: R122G, R123S, A124H, I125M, D126L, R127E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Plasmid: PRSET-C / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K-12 / References: UniProt: P10955
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.54 Å3/Da / Density % sol: 22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 4000, Acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
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: Dec 20, 1998 / Details: MIRROR/MONOCHROMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.1→100 Å / Num. all: 41962 / Num. obs: 41962 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 21.1
Reflection shellResolution: 1.1→1.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.455 / Num. unique all: 890 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 216753
Reflection shell
*PLUS
% possible obs: 87.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
RefinementResolution: 1.4→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1040 4.9 %RANDOM
Rwork0.224 ---
all-21313 --
obs-21313 98.9 %-
Displacement parametersBiso mean: 18.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 43 73 1135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_improper_angle_d1.14
X-RAY DIFFRACTIONx_mcbond_it1.31.5
X-RAY DIFFRACTIONx_mcangle_it2.112
X-RAY DIFFRACTIONx_scbond_it2.142
X-RAY DIFFRACTIONx_scangle_it3.182.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 180 5.2 %
Rwork0.325 3298 -
obs--97.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.278 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.46 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.479
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.14

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