SAXSdb — 1d06

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

nitrogen fixation regulatory protein fixL

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 122–251	Mutation：R122G, R123S, A124H, I125M, D126L, R127E	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；PEG 4000, Acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 1.40 Å R-free 0.275
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 122–251	Mutation：R122G, R123S, A124H, I125M, D126L, R127E	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；PEG 4000, Acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 1.40 Å R-free 0.275

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 1D06	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EW0 CRYSTAL STRUCTURE ANALYSIS OF THE SENSOR DOMAIN OF RMFIXL(FERROUS FORM) Deposited 2000-04-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 122–251（130 aa） Fragment：SENSOR DOMAIN	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG 4000, acetic acid/NaOH, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.265

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FIXL_RHIME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 122–251

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	1d06
Deposition date deposition_date	1999-09-09
Structure title title	STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION
Keywords keywords	OXYGEN SENSOR, HISTIDINE KINASE, PAS, HIGH-RESOLUTION, TWO-COMPONENT SYSTEM, SIGNALING PROTEIN; SIGNALING PROTEIN
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	17.43 Å
Radius of gyration Rg (electron density) rg_electron	16.32 Å
Forward intensity I(0) i0	4693440.00
Molecular weight molecular_weight	15116.0 kDa
Excluded volume excluded_volume	18736 Å³
Envelope volume envelope_volume	21739 Å³
Hydration-shell volume shell_volume	12301 Å³
Envelope diameter envelope_diameter	61.2 Å
Shell Rg shell_rg	21.26 Å
Envelope Rg envelope_rg	17.09 Å
Shape Rg shape_rg	16.27 Å
Total Rg total_rg	17.37 Å
Total atoms total_atoms	1062
Residues n_residues	130
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	62.2 Å
Rg (real space) rg_real	17.57 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	4.6930e+06
I(0) uncertainty (real space) i0_real_error	6.3510e+04
Rg (reciprocal space) rg_reciprocal	17.56 Å
I(0) (reciprocal space) i0_reciprocal	4693000.0000
Solution quality estimate total_estimate	0.8156
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.621
Kurtosis Kurtosis kurtosis	0.179
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	628400.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.610; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.928

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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	nitrogen fixation regulatory protein fixL
Molecular weight formula_weight	14522.4 kDa
Mutation mutation	R122G, R123S, A124H, I125M, D126L, R127E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1135

GSHMLETEDVVRARDAHLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQRYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRSGGERFFTGFIRDLT

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 K12

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 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	73

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d06a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.2 — Heme-binding PAS domain

CATH v4.4 (1 domains)

Domain ID domain_id	1d06A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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8. Citations (1)

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Unit-cell length a length_a	60.600 Å
Unit-cell length b length_b	37.150 Å
Unit-cell length c length_c	53.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2750

fit	/app/data/saxs_computation/d0/1d06/1d06.fit
pddf	/app/data/pr_computation/d0/1d06/1d06.pr.out
profile	/app/data/saxs_computation/d0/1d06/1d06.dat

STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION

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

nitrogen fixation regulatory protein fixL

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