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2m5j

Solution structure of the periplasmic signaling domain of HasR, a TonB-dependent outer membrane heme transporter

Method: SOLUTION NMR Dmax: 50.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HasR protein

Serratia marcescens

UniProt Q79AD2

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 42–146 Fragment：UNP residues 42-146 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；293 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1 NMR sample composition：0.5 mM [U-99% 13C; U-99% 15N] HasR_N-terminal_periplasmic_signaling_domain-1, 50 mM Sodium phosphate-2, 50 mM NaCl-3, 85% H2O/15% D2O | 85% H2O/15% 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 2M5J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3CSL Structure of the Serratia marcescens hemophore receptor HasR in complex with its hemophore HasA and heme Deposited 2008-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 35–899（865 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.70 Å R-free 0.274
3CSL Structure of the Serratia marcescens hemophore receptor HasR in complex with its hemophore HasA and heme Deposited 2008-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 35–899（865 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.70 Å R-free 0.274
3CSN Structure of the Serratia marcescens hemophore receptor HasR in complex with its hemophore HasA Deposited 2008-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 35–899（865 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；291 K；2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.244
3CSN Structure of the Serratia marcescens hemophore receptor HasR in complex with its hemophore HasA Deposited 2008-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 35–899（865 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；291 K；2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.244
3DDR Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme Deposited 2008-06-06 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 × 2 PDB declaration: dimeric
Chain A 48–899（852 aa） Fragment：UNP residues 48 to 899
Mutation：I671G NA SODIUM ION × 1 GOL GLYCEROL × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；291 K；2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.262
3DDR Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme Deposited 2008-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 48–899（852 aa） Fragment：UNP residues 48 to 899
Mutation：I671G NA SODIUM ION × 1 GOL GLYCEROL × 5 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；291 K；2 M NaCl, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.262
5C58 A double mutant of serratia marcescens hemophore receptor HasR in complex with its hemophore HasA and heme Deposited 2015-06-19 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 × 2 PDB declaration: dimeric
Chain A 35–899（865 aa）
Mutation：R297A, N800A HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100mM Tris pH 7 to 8, 1.8 to 2.2mM NaCl, 100mM K2HPO4
Resolution 2.79 Å R-free 0.296

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

View Construct and Data Evidence
UniProt name Q79AD2_SERMA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–107； UniProt 42–146

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 2m5j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2m5j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2m5j
Deposition date deposition_date2013-02-26
Structure title titleSolution structure of the periplasmic signaling domain of HasR, a TonB-dependent outer membrane heme transporter
Keywords keywordssignaling domain, TonB dependent transporter, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.49 Å
Radius of gyration Rg (electron density) rg_electron14.10 Å
Forward intensity I(0) i0745495000.00
Molecular weight molecular_weight221990.0 kDa
Excluded volume excluded_volume274820 ų
Envelope volume envelope_volume34400 ų
Hydration-shell volume shell_volume16987 ų
Envelope diameter envelope_diameter56.4 Å
Shell Rg shell_rg23.28 Å
Envelope Rg envelope_rg17.40 Å
Shape Rg shape_rg14.09 Å
Total Rg total_rg14.35 Å
Total atoms total_atoms31160
Residues n_residues2140
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 dmax50.9 Å
Rg (real space) rg_real14.43 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real7.4550e+08
I(0) uncertainty (real space) i0_real_error8.8620e+06
Rg (reciprocal space) rg_reciprocal14.44 Å
I(0) (reciprocal space) i0_reciprocal745500000.0000
Solution quality estimate total_estimate0.8495
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.1 Å
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.286
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha264000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.684; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 1.000
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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_id2m5jA00
Class class3 — Alpha Beta
Architecture architecture55 — 3-Layer(bab) Sandwich
Topology topology50 — Phage tail protein beta-alpha-beta fold
Homologous superfamily homologous superfamily30 —
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8. Citations (1)

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9. Files and Curves (10)