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1ybj

Structural and Dynamics studies of both apo and holo forms of the hemophore HasA

Method: SOLUTION NMR Dmax: 63.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–179 Not recorded No other associated polymer 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

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 1YBJ 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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
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 method 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 ligand/ion Different experimental method 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 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 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 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 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 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 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 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 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
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 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 C 2–188（187 aa）
Not recorded 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 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 D 2–188（187 aa）
Not recorded 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 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 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HASA_SERMA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–178； UniProt 2–179

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 1ybj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ybj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ybj
Deposition date deposition_date2004-12-21
Structure title titleStructural and Dynamics studies of both apo and holo forms of the hemophore HasA
Keywords keywordsalpha+beta structure, curved anti-parallel beta-sheet, METAL BINDING PROTEIN; METAL BINDING 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_guinier16.58 Å
Radius of gyration Rg (electron density) rg_electron15.94 Å
Forward intensity I(0) i0519075000.00
Molecular weight molecular_weight182690.0 kDa
Excluded volume excluded_volume224040 ų
Envelope volume envelope_volume49498 ų
Hydration-shell volume shell_volume21338 ų
Envelope diameter envelope_diameter69.9 Å
Shell Rg shell_rg26.04 Å
Envelope Rg envelope_rg19.29 Å
Shape Rg shape_rg15.93 Å
Total Rg total_rg16.24 Å
Total atoms total_atoms24770
Residues n_residues1780
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 dmax63.9 Å
Rg (real space) rg_real16.50 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real5.1910e+08
I(0) uncertainty (real space) i0_real_error6.2520e+06
Rg (reciprocal space) rg_reciprocal16.51 Å
I(0) (reciprocal space) i0_reciprocal519100000.0000
Solution quality estimate total_estimate0.8031
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.9 Å
Skewness Skewness skewness0.265
Kurtosis Kurtosis kurtosis-0.241
Angular range angular_range— – 0.4800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4014000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.509; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ybja_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.35 — Heme-binding protein A (HasA)
Superfamily Superfamily superfamilyd.35.1 — Heme-binding protein A (HasA)
Family Family familyd.35.1.1 — Heme-binding protein A (HasA)

CATH v4.4 (1 domains)

Domain ID domain_id1ybjA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1500 — Heme-binding Protein A; Chain: A;
Homologous superfamily homologous superfamily10 — Haem-binding HasA
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8. Citations (1)

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9. Files and Curves (10)