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1d5w

PHOSPHORYLATED FIXJ RECEIVER DOMAIN

Method: X-RAY DIFFRACTION Dmax: 92.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ

Sinorhizobium meliloti

UniProt P10958

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–126 Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126) Mutation：T2Q, A125L Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；AMMONIUM SULFATE, 2-METHYL-2,4-PENTANEDIOL, HEPES, TRITON X-100, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.30 Å R-free 0.244
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–126 Chain C； UniProt 1–126 Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126) Mutation：T2Q, A125L Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；AMMONIUM SULFATE, 2-METHYL-2,4-PENTANEDIOL, HEPES, TRITON X-100, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.30 Å R-free 0.244

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1D5W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DBW CRYSTAL STRUCTURE OF FIXJ-N Deposited 1999-11-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)
Mutation：T2Q, A125L 15P POLYETHYLENE GLYCOL (N=34) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 1.60 Å R-free 0.224
1DBW CRYSTAL STRUCTURE OF FIXJ-N Deposited 1999-11-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)
Mutation：T2Q, A125L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 1.60 Å R-free 0.224
1DCK STRUCTURE OF UNPHOSPHORYLATED FIXJ-N COMPLEXED WITH MN2+ Deposited 1999-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–126（126 aa） Fragment：N-TERMINAL DOMAIN (RESIDUES 1-126)
Mutation：T2Q, A125L MN MANGANESE (II) ION × 1 15P POLYETHYLENE GLYCOL (N=34) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 2.00 Å R-free 0.253
1DCK STRUCTURE OF UNPHOSPHORYLATED FIXJ-N COMPLEXED WITH MN2+ Deposited 1999-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–126（126 aa） Fragment：N-TERMINAL DOMAIN (RESIDUES 1-126)
Mutation：T2Q, A125L MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 2.00 Å R-free 0.253
1DCM STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A) Deposited 1999-11-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)
Mutation：T2Q, A125L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；PEG1500, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 3.00 Å R-free 0.335
1DCM STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A) Deposited 1999-11-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)
Mutation：T2Q, A125L MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；PEG1500, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 3.00 Å R-free 0.335
1X3U Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot Deposited 2005-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 130–204（75 aa） Fragment：C-TERMINAL DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Pressure 1
NMR sample composition 1mM FixJC U-15N,13C; 20mM NaHPO4-NaH2PO4 (pH 5.5), 100mM NaCl, 50mM Na2SO4; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIXJ_RHIME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–126； UniProt 1–126 Author chain B； PDBConstruct 1–126； UniProt 1–126 Author chain C； PDBConstruct 1–126； UniProt 1–126

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1d5w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d5w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d5w
Deposition date deposition_date1999-10-12
Structure title titlePHOSPHORYLATED FIXJ RECEIVER DOMAIN
Keywords keywordsDOUBLY WOUND FIVE-STRANDED BETA/ALPHA FOLD, PHOSPHORYLATED PROTEIN, NITROGEN FIXATION REGULATION, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.16 Å
Radius of gyration Rg (electron density) rg_electron26.93 Å
Forward intensity I(0) i028573200.00
Molecular weight molecular_weight40609.0 kDa
Excluded volume excluded_volume50604 ų
Envelope volume envelope_volume63068 ų
Hydration-shell volume shell_volume21766 ų
Envelope diameter envelope_diameter97.5 Å
Shell Rg shell_rg31.32 Å
Envelope Rg envelope_rg26.94 Å
Shape Rg shape_rg26.90 Å
Total Rg total_rg27.53 Å
Total atoms total_atoms2834
Residues n_residues364
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.8 Å
Rg (real space) rg_real27.53 Å
Rg uncertainty (real space) rg_real_error0.72 Å
I(0) (real space) i0_real2.8570e+07
I(0) uncertainty (real space) i0_real_error4.2230e+05
Rg (reciprocal space) rg_reciprocal27.42 Å
I(0) (reciprocal space) i0_reciprocal28570000.0000
Solution quality estimate total_estimate0.5802
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary22.4 Å
Skewness Skewness skewness0.576
Kurtosis Kurtosis kurtosis-0.385
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha17840000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 0.051; Positv: 1.000; Valcen: 0.625; Smooth: 0.900
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1d5wa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related
Domain ID domain_idd1d5wb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related
Domain ID domain_idd1d5wc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related

CATH v4.4 (3 domains)

Domain ID domain_id1d5wA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1d5wB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1d5wC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (1)

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9. Files and Curves (10)