SAXSdb — 3ddr

▼

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

HasR protein

Serratia marcescens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 48–899	Fragment：UNP residues 48 to 899 Mutation：I671G	Hemophore HasA × 1 （Q54450） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 48–899	Fragment：UNP residues 48 to 899 Mutation：I671G	Hemophore HasA × 1 （Q54450） 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

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 3DDR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M5J Solution structure of the periplasmic signaling domain of HasR, a TonB-dependent outer membrane heme transporter Deposited 2013-02-26	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 42–146（105 aa） Fragment：UNP residues 42-146	Not recorded	No recorded non-water small molecule	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
3CSL Structure of the Serratia marcescens hemophore receptor HasR in complex with its hemophore HasA and heme Deposited 2008-04-10	Different construct Different mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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
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 ligand/ion 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 6 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 14–865； UniProt 48–899 Author chain B； PDBConstruct 14–865； UniProt 48–899

Hemophore HasA

Serratia marcescens

UniProt Q54450

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–188	Not recorded	HasR protein × 1 （Q79AD2） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 2–188	Not recorded	HasR protein × 1 （Q79AD2） 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

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 3DDR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B2V HEME-BINDING PROTEIN A Deposited 1998-12-01	Different construct 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 1–188（188 aa）	Not recorded	CA CALCIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.2M CACL, 0.1M NA ACETATE PH 4.6, 20% ISOPRPANOL	Resolution 1.90 Å R-free 0.218
1DK0 CRYSTAL STRUCTURE OF THE HEMOPHORE HASA FROM SERRATIA MARCESCENS CRYSTAL FORM P2(1), PH8 Deposited 1999-12-06	Different construct 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 1–188（188 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M NaHepes, pH8.0, 1.4M NaKTartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.77 Å R-free 0.213
1DK0 CRYSTAL STRUCTURE OF THE HEMOPHORE HASA FROM SERRATIA MARCESCENS CRYSTAL FORM P2(1), PH8 Deposited 1999-12-06	Different construct 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 1–188（188 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M NaHepes, pH8.0, 1.4M NaKTartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.77 Å R-free 0.213
1DKH CRYSTAL STRUCTURE OF THE HEMOPHORE HASA, PH 6.5 Deposited 1999-12-07	Different construct 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 1–188（188 aa）	Not recorded	ZN ZINC ION × 3 SM SAMARIUM (III) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Cacodylate buffer pH6.5, Zinc Acetate 140mM, Glycerol 2%, PEG8000 10%, Samarium Chloride 10mM., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.288
1YBJ Structural and Dynamics studies of both apo and holo forms of the hemophore HasA Deposited 2004-12-21	Different construct 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 2–179（178 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.6；303 K；Ionic strength (raw mmCIF value) 20mM sodium phosphate buffer；Pressure ambient NMR sample composition 1.8mM HasA 15N \| 20mM sodium phosphate buffer, pH5.6; 90% H2O/10% D20 NMR sample composition 1.9mM HasA 15N,13C \| 20mM sodium phosphate buffer, pH5.6; 90% H2O/10% D20	Resolution not provided
2CN4 The crystal structure of the secreted dimeric form of the hemophore HasA reveals a domain swapping with an exchanged heme ligand Deposited 2006-05-18	Different construct 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 2–174（173 aa） Chain B 2–174（173 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；2 MICROLITERS PROTEIN (AT A CONCENTRATION OF ABOUT 4 MG/ML) WERE MIXED WITH 1 MICROLITER RESERVOIR CONSISTING OF 100 MM TRIS BUFFER AT PH 8.5, 2 M K2HPO4 AND 2 M NAH2PO4.	Resolution 2.30 Å R-free 0.224
2UYD Crystal structure of the SmHasA mutant H83A Deposited 2007-04-04	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 X 1–188（188 aa）	Mutation：YES	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ZN ZINC ION × 8 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；293 K；DROPS WERE PREPARED BY MIXING 2MICROL OF THE PROTEIN SOLUTION WITH 1 MICROL OF THE RESERVOIR SOLUTION THAT CONTAINED 100 MM SODIUM CACODYLATE AT PH 6.5, 200 MM ZN(OAC)2 AND 10 % (V/V) 2-PROPANOL. THE BROWNISH CRYSTALS GREW OVER A PERIOD OF 2 MONTHS AT 20 DEGREES C.	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 ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–188（187 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 ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–188（187 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 ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–188（187 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 ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–188（187 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
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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–188（187 aa） Fragment：UNP residues 2-188	Not recorded	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
9XOH Crystal Structure of Redesigned HasAsm Variant (14-mutation) with Iron Tetraphenylporphyrin Deposited 2025-11-13	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 1–176（176 aa）	Mutation：A2S, G13A, H17A, G21T, S42T, Q63N, N79S, D102T, V110N, D112E, A125S, V131E, G145S, D156K	MQP [5,10,15,20-tetraphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]iron × 1 GOL GLYCEROL × 3 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M sodium cacodylate-HCl, 1M sodium citrate tribasic	Resolution 1.51 Å R-free 0.234
9XOH Crystal Structure of Redesigned HasAsm Variant (14-mutation) with Iron Tetraphenylporphyrin Deposited 2025-11-13	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 1–176（176 aa）	Mutation：A2S, G13A, H17A, G21T, S42T, Q63N, N79S, D102T, V110N, D112E, A125S, V131E, G145S, D156K	MQP [5,10,15,20-tetraphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]iron × 1 GOL GLYCEROL × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M sodium cacodylate-HCl, 1M sodium citrate tribasic	Resolution 1.51 Å R-free 0.234
9XOH Crystal Structure of Redesigned HasAsm Variant (14-mutation) with Iron Tetraphenylporphyrin Deposited 2025-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–176（176 aa）	Mutation：A2S, G13A, H17A, G21T, S42T, Q63N, N79S, D102T, V110N, D112E, A125S, V131E, G145S, D156K	MQP [5,10,15,20-tetraphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]iron × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M sodium cacodylate-HCl, 1M sodium citrate tribasic	Resolution 1.51 Å R-free 0.234
9XOH Crystal Structure of Redesigned HasAsm Variant (14-mutation) with Iron Tetraphenylporphyrin Deposited 2025-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–176（176 aa）	Mutation：A2S, G13A, H17A, G21T, S42T, Q63N, N79S, D102T, V110N, D112E, A125S, V131E, G145S, D156K	MQP [5,10,15,20-tetraphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]iron × 1 GOL GLYCEROL × 2 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M sodium cacodylate-HCl, 1M sodium citrate tribasic	Resolution 1.51 Å R-free 0.234
9XOK Crystal Structure of Redesigned HasAsm Variant (51-mutation) with Iron Tetraphenylporphyrin Deposited 2025-11-13	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 3–173（171 aa）	Mutation：;F11L, G12D, G13N, Y14L, S15T, I16L, H17Q, D18E, Y19F, L20F, G21N, Q22E, S25A, T26S, S58T, A61K, N62D, Q63G, Q88T, S93A, D96N, D102S, T103S, S104T, Q109T, V110E, D112Q, V113F, S114R, F115L, N119G, L120W, S121T, L123E, Q124I, A125S, Q126E, T144S, G145T, A146P, E148L, T149Q, G153N, I154Q, D156Q, D157Q, V162T, D167M, Q168E, V169I, A170R ;	MQP [5,10,15,20-tetraphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]iron × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M sodium cacodylate-HCl, 2M ammonium sulfate, 0.2M NaCl	Resolution 1.80 Å R-free 0.330
9XPD Crystal Structure of Redesigned HasAsm Variant (51-mutation) with Heme Deposited 2025-11-16	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 1–176（176 aa）	Mutation：;F11L, G12D, G13N, Y14L, S15T, I16L, H17Q, D18E, Y19F, L20F, G21N, Q22E, S25A, T26S, S58T, A61K, N62D, Q63G, Q88T, S93A, D96N, D102S, T103S, S104T, Q109T, V110E, D112Q, V113F, S114R, F115L, N119G, L120W, S121T, L123E, Q124I, A125S, Q126E, T144S, G145T, A146P, E148L, T149Q, G153N, I154Q, D156Q, D157Q, V162T, D167M, Q168E, V169I, A170R ;	IMD IMIDAZOLE × 1 CIT CITRIC ACID × 1 GOL GLYCEROL × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M imidazole-HCl, 1M sodium citrate tribasic	Resolution 1.22 Å R-free 0.177
9XPI Crystal Structure of Redesigned HasAsm Variant (48-mutation) with Heme Deposited 2025-11-16	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 1–176（176 aa）	Mutation：;F11L, G12A, G13N, Y14L, S15T, I16L, H17A, D18E, Y19F, L20F, G21N, Q22E, T26Y, N41S, S58T, A61K, N62D, Q63G, N79S, E80P, Q88T, S91A, S93T, D96N, T103S, S104T, Q109V, V110N, D112E, S114T, G116S, L120W, S121T, L123E, A125E, Q126E, Q134K, V136I, G145T, E148L, T149Q, G153S, I154L, D156K, D157Q, V162I, Q168E, V169I ;	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ACT ACETATE ION × 3 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M imidazole-HCl, 2.5M NaCl, 0.2M Zinc acetate	Resolution 2.16 Å R-free 0.255

13 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HASA_SERMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 20–206； UniProt 2–188 Author chain D； PDBConstruct 20–206； UniProt 2–188

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ddr
Deposition date deposition_date	2008-06-06
Structure title title	Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme
Keywords keywords	;outer membrane protein, beta-barrel, hemophore receptor, Membrane, Outer membrane, TonB box, Heme, Iron, Metal-binding, Secreted, MEMBRANE PROTEIN-HEME BINDING PROTEIN COMPLEX ;; MEMBRANE PROTEIN/HEME BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	52.56 Å
Radius of gyration Rg (electron density) rg_electron	52.84 Å
Forward intensity I(0) i0	628660000.00
Molecular weight molecular_weight	201600.0 kDa
Excluded volume excluded_volume	248690 Å³
Envelope volume envelope_volume	345900 Å³
Hydration-shell volume shell_volume	56274 Å³
Envelope diameter envelope_diameter	187.1 Å
Shell Rg shell_rg	53.71 Å
Envelope Rg envelope_rg	52.09 Å
Shape Rg shape_rg	52.84 Å
Total Rg total_rg	52.86 Å
Total atoms total_atoms	14246
Residues n_residues	1830
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

▼

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

Maximum dimension Dmax dmax	178.6 Å
Rg (real space) rg_real	53.01 Å
Rg uncertainty (real space) rg_real_error	2.39 Å
I(0) (real space) i0_real	6.2870e+08
I(0) uncertainty (real space) i0_real_error	1.3180e+07
Rg (reciprocal space) rg_reciprocal	52.17 Å
I(0) (reciprocal space) i0_reciprocal	627900000.0000
Solution quality estimate total_estimate	0.7581
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	35.7 Å
Skewness Skewness skewness	0.468
Kurtosis Kurtosis kurtosis	-0.508
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	128100000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.524; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.745; Smooth: 0.540

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	HasR protein
Molecular weight formula_weight	94898.6 kDa
Mutation mutation	I671G
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	14259

AQAEASSAQAAQQKNFNIAAQPLQSAMLRFAEQAGMQVFFDEVKLDGMQAAALNGSMSVEQGLRRLIGGNPVAFRLQPQGQIVLSRLPTANGDGGALALDSLTVLGAGGNNANDWVYDEPRSVSVISREQMDNRPARHAADILEQTTGAYSSVSQQDPALSVNIRGIQDYGRVNMNIDGMRQNFQKSGHGQRNGTMYIDSELLSGVTIDKGTTGGMGSAGTLGGIATFNTVSASDFLAPGKELGGKLHASTGDNGTHFIGSGILALGNETGDILLAASERHLGDYWPGNKGDIGNIRINNDTGNYDRYAESIKNNKIPDTHYRMHSRLAKVGWNLPANQRLQLSYLQTQTASPIAGTLTNLGTRPPYELGWKRTGYTDVMARNAAFDYSLAPEDVDWLDFQAKLYYVDTQDDSDTYSTSSLLDNGYATRTRLRTYGAQAQNTSRFSLAPGHDFRANYGLEFYYDKATSDSSRQGMEGVTPAGNRSVASLFANLTYDYDGWLTLEGGLRYDRYRLRGQTGLSYPDLAKDGQRYTIDNPCKALRLTGCSTTTREDWDVDRDQGKLSPTLAVAVRPGVEWLELYTTYGKSWRPPAITETLTNGSAHSSSTQYPNPFLQPERSRAWEVGFNVQQPDLWFEGDRLVAKVAYFDTKVDNYINLAIDRNKPGLVQPSGGNAAYVNNLSKTRFRGLEYQLNYDAGVFYADLTYTHMIGKNEFCSNKAWLGGRLRYGDGSRRGNFYVEPDAASNDFVTCDGGTQFGSAAYLPGDRGSVTLGGRAFDRKLDAGVTVRFAPGYQDSSVPSNYPYLADWPKYTLFDLYASYKLTDSLTLRGSVENLTNRAYVVSYGETLANTLGRGRTVQGGVEYRF

来源 Source

来源生物 organism	Serratia marcescens
NCBI Class编号 ncbi_taxonomy_id	615
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Hemophore HasA
Molecular weight formula_weight	21523.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MRGSHHHHHHGIRMRARYPAFSVNYDSSFGGYSIHDYLGQWASTFGDVNHTNGNVTDANSGGFYGGSLSGSQYAISSTANQVTAFVAGGNLTYTLFNEPAHTLYGQLDSLSFGDGLSGGDTSPYSIQVPDVSFGGLNLSSLQAQGHDGVVHQVVYGLMSGDTGALETALNGILDDYGLSVNSTFDQVAAATAVGVQHADSPELLAA

来源 Source

来源生物 organism	Serratia marcescens
NCBI Class编号 ncbi_taxonomy_id	615
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

▼

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3ddrc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.35 — Heme-binding protein A (HasA)
Superfamily Superfamily superfamily	d.35.1 — Heme-binding protein A (HasA)
Family Family family	d.35.1.1 — Heme-binding protein A (HasA)

Domain ID domain_id	d3ddrc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ddrd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.35 — Heme-binding protein A (HasA)
Superfamily Superfamily superfamily	d.35.1 — Heme-binding protein A (HasA)
Family Family family	d.35.1.1 — Heme-binding protein A (HasA)

Domain ID domain_id	d3ddrd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	3ddrA01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

Domain ID domain_id	3ddrA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

Domain ID domain_id	3ddrB01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

Domain ID domain_id	3ddrB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

Domain ID domain_id	3ddrC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1500 — Heme-binding Protein A; Chain: A;
Homologous superfamily homologous superfamily	10 — Haem-binding HasA

Domain ID domain_id	3ddrD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1500 — Heme-binding Protein A; Chain: A;
Homologous superfamily homologous superfamily	10 — Haem-binding HasA

▶

8. Citations (1)

▶

Unit-cell length a length_a	157.410 Å
Unit-cell length b length_b	162.720 Å
Unit-cell length c length_c	597.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	39.250 Å
R factor r_factor	0.2270
R_work r_work	0.2260
R_free r_free	0.2620

fit	/app/data/saxs_computation/dd/3ddr/3ddr.fit
pddf	/app/data/pr_computation/dd/3ddr/3ddr.pr.out
profile	/app/data/saxs_computation/dd/3ddr/3ddr.dat

Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme

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

HasR protein

State in the Current Structure

Other States of the Same Protein in the Database

Hemophore HasA

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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)