SAXSdb — 2lhr

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

Iron-regulated surface determinant protein H

Staphylococcus aureus subsp. aureus

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 467–543	Fragment：UNP residues 467-543	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 140；Pressure ambient NMR sample composition：1.1 mM [U-100% 15N] IsdH linker, 20 mM potassium phosphate, 50 mM potassium chloride, 100 uM AEBSF protease inhibitor, 0.01 % sodium azide, 7 % D2O, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：1.3 mM [U-100% 13C; U-100% 15N] IsdH linker, 20 mM potassium phosphate, 50 mM potassium chloride, 100 uM AEBSF protease inhibitor, 0.01 % sodium azide, 7 % D2O, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：1.3 mM [U-100% 13C; U-100% 15N] IsdH linker, 20 mM potassium phosphate, 50 mM potassium chloride, 100 uM AEBSF protease inhibitor, 0.01 % sodium azide, 100 % D2O, 100% D2O \| 100% D2O	Resolution not provided

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 2LHR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SZK Crystal Structure of Human metHaemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus aureus Deposited 2011-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 86–229（144 aa） Fragment：first NEAT domain	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M potassium thiocyanate, 0.1M Tris-bis propane, 20% PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.275
3SZK Crystal Structure of Human metHaemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus aureus Deposited 2011-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 86–229（144 aa） Fragment：first NEAT domain	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M potassium thiocyanate, 0.1M Tris-bis propane, 20% PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.275
4FC3 Crystal Structure of Human Methaemoglobin Complexed with the Second NEAT Domain of IsdH from Staphylococcus aureus Deposited 2012-05-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 321–464（144 aa） Fragment：Second NEAT domain	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M Sodium formate, 0.1M bis-tris propane, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.26 Å R-free 0.256
9S3P Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 3IsdH(alpha2beta):Hbtet complex Deposited 2025-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 326–665（340 aa） Chain F 326–665（340 aa） Chain G 326–665（340 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；blot time 3 s	Resolution 3.10 Å
9S4F Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 right tail Deposited 2025-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 326–665（340 aa） Chain D 326–665（340 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；blot time 3 s	Resolution 4.20 Å
9S4I Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 0 left tail Deposited 2025-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 326–665（340 aa） Chain D 326–665（340 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；blot time 3 s	Resolution 4.00 Å
9S4J Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 0 right tail Deposited 2025-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 326–665（340 aa） Chain D 326–665（340 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；blot time 3 s	Resolution 4.10 Å
9S4K Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 left tail Deposited 2025-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 326–665（340 aa） Chain D 326–665（340 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；blot time 3 s	Resolution 4.00 Å
9SZW Human carboxyhemoglobin bound to full-length Staphylococcus aureus IsdH - IsdH:Hbdim complex Deposited 2025-10-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 86–665（580 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；blot time 3 s	Resolution 3.14 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ISDH_STAAW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–78； UniProt 467–543

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	2lhr
Deposition date deposition_date	2011-08-12
Structure title title	Solution structure of Staphylococcus aureus IsdH linker domain
Keywords keywords	Heme acquisition, Iron uptake, NEAT domain, Hemoglobin receptor, METAL TRANSPORT; METAL TRANSPORT
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	18.44 Å
Radius of gyration Rg (electron density) rg_electron	17.73 Å
Forward intensity I(0) i0	476469000.00
Molecular weight molecular_weight	185250.0 kDa
Excluded volume excluded_volume	232400 Å³
Envelope volume envelope_volume	48662 Å³
Hydration-shell volume shell_volume	17513 Å³
Envelope diameter envelope_diameter	86.8 Å
Shell Rg shell_rg	30.20 Å
Envelope Rg envelope_rg	27.26 Å
Shape Rg shape_rg	17.75 Å
Total Rg total_rg	18.03 Å
Total atoms total_atoms	26040
Residues n_residues	1560
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	49.7 Å
Rg (real space) rg_real	16.93 Å
Rg uncertainty (real space) rg_real_error	0.14 Å
I(0) (real space) i0_real	4.5320e+08
I(0) uncertainty (real space) i0_real_error	4.8020e+06
Rg (reciprocal space) rg_reciprocal	18.84 Å
I(0) (reciprocal space) i0_reciprocal	476500000.0000
Solution quality estimate total_estimate	0.6630
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.420
Kurtosis Kurtosis kurtosis	-0.556
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	3.1170
Highest regularization parameter α highest_alpha	94330.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.006; Oscil: 0.947; Stabil: 0.983; Sysdev: 0.000; Positv: 1.000; Valcen: 0.837; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2lhrA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1270 —

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8. Citations (1)

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Description description	Iron-regulated surface determinant protein H
Molecular weight formula_weight	9280.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	26040

来源生物 organism	Staphylococcus aureus subsp. aureus
NCBI Class编号 ncbi_taxonomy_id	196620
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/lh/2lhr/2lhr.fit
pddf	/app/data/pr_computation/lh/2lhr/2lhr.pr.out
profile	/app/data/saxs_computation/lh/2lhr/2lhr.dat

Solution structure of Staphylococcus aureus IsdH linker domain

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

Iron-regulated surface determinant protein H

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)