SAXSdb — 1dcm

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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ

Sinorhizobium meliloti

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–126	Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126) Mutation：T2Q, A125L	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–126	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

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 1DCM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5W PHOSPHORYLATED FIXJ RECEIVER DOMAIN Deposited 1999-10-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–126（126 aa） 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
1D5W PHOSPHORYLATED FIXJ RECEIVER DOMAIN Deposited 1999-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126) Chain C 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L Non-standard monomer：Yes (specific site not provided by mmCIF) 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
1DBW CRYSTAL STRUCTURE OF FIXJ-N Deposited 1999-11-03	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 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 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 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
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 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dcm
Deposition date deposition_date	1999-11-05
Structure title title	STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A)
Keywords keywords	DOUBLY WOUND FIVE-STRANDED BETA/ALPHA FOLD, NITROGEN FIXATION REGULATION, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.96 Å
Radius of gyration Rg (electron density) rg_electron	21.24 Å
Forward intensity I(0) i0	11307300.00
Molecular weight molecular_weight	25583.0 kDa
Excluded volume excluded_volume	32124 Å³
Envelope volume envelope_volume	40251 Å³
Hydration-shell volume shell_volume	16712 Å³
Envelope diameter envelope_diameter	71.5 Å
Shell Rg shell_rg	26.43 Å
Envelope Rg envelope_rg	21.20 Å
Shape Rg shape_rg	21.26 Å
Total Rg total_rg	21.92 Å
Total atoms total_atoms	1794
Residues n_residues	242
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	69.2 Å
Rg (real space) rg_real	22.05 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.1310e+07
I(0) uncertainty (real space) i0_real_error	1.3460e+05
Rg (reciprocal space) rg_reciprocal	22.04 Å
I(0) (reciprocal space) i0_reciprocal	11310000.0000
Solution quality estimate total_estimate	0.8783
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	0.385
Kurtosis Kurtosis kurtosis	-0.608
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5827000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ
Molecular weight formula_weight	13880.0 kDa
Mutation mutation	T2Q, A125L
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1806

MQDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLVALE

来源 Source

来源生物 organism	Sinorhizobium meliloti
NCBI Class编号 ncbi_taxonomy_id	382
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dcma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

Domain ID domain_id	d1dcmb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

CATH v4.4 (2 domains)

Domain ID domain_id	1dcmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	1dcmB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (2)

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Unit-cell length a length_a	115.600 Å
Unit-cell length b length_b	34.800 Å
Unit-cell length c length_c	66.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	14.920 Å
R factor r_factor	0.2480
R_work r_work	0.2480
R_free r_free	0.3350

fit	/app/data/saxs_computation/dc/1dcm/1dcm.fit
pddf	/app/data/pr_computation/dc/1dcm/1dcm.pr.out
profile	/app/data/saxs_computation/dc/1dcm/1dcm.dat

STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A)

1. Protein Identity and Related Structures Protein Identity & Related Structures

TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction