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3m4z

Crystal Structure of B. subtilis ferrochelatase with Cobalt bound at the active site

Method: X-RAY DIFFRACTION Dmax: 67.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferrochelatase

Bacillus subtilis

UniProt P32396

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 2–310 Not recorded CO COBALT (II) ION × 1 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% PEG 2000, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.94 Å R-free 0.199

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 3M4Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AK1 FERROCHELATASE FROM BACILLUS SUBTILIS Deposited 1997-05-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions seeded；pH 8.5；CRYSTALS GROW IN 30% PEG 2000, 0.2 M MGCL2 0.1 M TRIS-HCL, PH 8.5. THESE WERE VORTEXED AND USED AS SEEDS FOR LARGE SINGLE CRYSTALS IN: 27% PEG 2000, 0.2 M MGCL2, 0.05% NAN3, 0.1 M TRIS-HCL, PH 8.5, seeded
Resolution 1.90 Å R-free 0.243
1C1H CRYSTAL STRUCTURE OF BACILLUS SUBTILIS FERROCHELATASE IN COMPLEX WITH N-METHYL MESOPORPHYRIN Deposited 1999-07-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Not recorded MG MAGNESIUM ION × 1 MMP N-METHYLMESOPORPHYRIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 2000, MAGNESIUM CHLORIDE, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP
Resolution 1.90 Å R-free 0.231
1C9E STRUCTURE OF FERROCHELATASE WITH COPPER(II) N-METHYLMESOPORPHYRIN COMPLEX BOUND AT THE ACTIVE SITE Deposited 1999-08-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 5–310（306 aa）
Not recorded MG MAGNESIUM ION × 1 MP1 N-METHYLMESOPORPHYRIN CONTAINING COPPER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；PEG 2000, magnesium chloride, TRIS, copper sulfate, N-methylmesoporphyrin, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.30 Å R-free 0.255
1DOZ CRYSTAL STRUCTURE OF FERROCHELATASE Deposited 1999-12-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–310（309 aa）
Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；PEG2000, MAGNESIUM CHLORIDE, TRIS, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 1.80 Å R-free 0.216
1LD3 Crystal Structure of B. subilis ferrochelatase with Zn(2+) bound at the active site. Deposited 2002-04-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 2000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.274
1N0I Crystal Structure of Ferrochelatase with Cadmium bound at active site Deposited 2002-10-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Not recorded CD CADMIUM ION × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；PEG2000, magnesium chloride, tris, pH 7.4, VAPOR DIFFUSION, temperature 298K
Resolution 2.00 Å R-free 0.273
2AC2 Crystal structure of the Tyr13Phe mutant variant of Bacillus subtilis Ferrochelatase with Zn(2+) bound at the active site Deposited 2005-07-18 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–310（309 aa）
Mutation：Y13F ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；288 K；PEG 2000, magnesium chloride, tris, pH 7.4, VAPOR DIFFUSION, temperature 288K
Resolution 2.50 Å R-free 0.257
2AC4 Crystal structure of the His183Cys mutant variant of Bacillus subtilis Ferrochelatase Deposited 2005-07-18 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–310（309 aa）
Mutation：H183C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；298 K；PEG 2000, magnesium chloride, tris, pH 7.4, VAPOR DIFFUSION, temperature 298K
Resolution 2.10 Å R-free 0.276
2H1V Crystal structure of the Lys87Ala mutant variant of Bacillus subtilis ferrochelatase Deposited 2006-05-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：K87A MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；288 K；25-30% PEG 2000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, temperature 288K
Resolution 1.20 Å R-free 0.173
2H1W Crystal structure of the His183Ala mutant variant of Bacillus subtilis ferrochelatase Deposited 2006-05-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：H183A FE2 FE (II) ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；288 K；25-30 % PEG2000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, temperature 288K
Resolution 2.60 Å R-free 0.259
2HK6 Crystal Structure of B. subtilis ferrochelatase with Iron bound at the active site Deposited 2006-07-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Not recorded FE FE (III) ION × 4 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；288 K；25% PEG 2000, 0.2 M MgCl2, 0.1 M Tris-HCl , pH 8.0, VAPOR DIFFUSION, temperature 288K
Resolution 1.71 Å R-free 0.220
2Q2N Crystal structure of Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride Deposited 2007-05-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–310（309 aa）
Not recorded MG MAGNESIUM ION × 2 H01 PROTOPORPHYRIN IX 2,4-DISULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；30% PEG 2000, 0.1M Tris/HCl pH 8, 0.2M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.80 Å R-free 0.250
2Q2O Crystal structure of H183C Bacillus subtilis ferrochelatase in complex with deuteroporphyrin IX 2,4-disulfonic acid dihydrochloride Deposited 2007-05-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–310（309 aa）
Mutation：H183C MG MAGNESIUM ION × 1 H01 PROTOPORPHYRIN IX 2,4-DISULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；30% PEG 2000, 0.1M Tris/HCl pH 8, 0.2M magnesium chloride, 0.1M spermin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.10 Å R-free 0.219
2Q3J Crystal structure of the His183Ala variant of Bacillus subtilis ferrochelatase in complex with N-Methyl Mesoporphyrin Deposited 2007-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–310（309 aa）
Mutation：H183A MG MAGNESIUM ION × 1 H02 N-METHYL PROTOPORPHYRIN IX 2,4-DISULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；25-30 % PEG 2000, 0.2 M MgCl2, 0.1 M TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.39 Å R-free 0.228
3GOQ Crystal structure of the Tyr13Met variant of Bacillus subtilis ferrochelatase Deposited 2009-03-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13M MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；25-30 % PEG 2000, 0.2 M MgCl2, 0.1 M TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.232
9KTA Bacillus subtilis CpfC (HemH) Y13C variant Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C MG MAGNESIUM ION × 5 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M MgCl2, 0.05M Bis-Tris, 12.5%(w/v) PEG3350
Resolution 1.00 Å R-free 0.190
9KTB Bacillus subtilis CpfC (HemH) Y13C variant modified with bromobimane Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C 9UM 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione × 1 MG MAGNESIUM ION × 5 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2, 0.1M Bis-Tris, 25%(w/v) PEG3000
Resolution 1.13 Å R-free 0.188
9KTC Mn(II)-bound CpfC (HemH) Y13C variant modified with bromobimane Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C 9UM 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione × 1 MG MAGNESIUM ION × 3 MN MANGANESE (II) ION × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2, 0.1M Bis-Tris, 30%(w/v) PEG3350, 4.5 mM MnCl2
Resolution 1.50 Å R-free 0.246
9KTD Fe(II)-bound CpfC (HemH) Y13C variant modified with bromobimane Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C MG MAGNESIUM ION × 2 CL CHLORIDE ION × 5 9UM 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione × 1 FE2 FE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2, 0.1M Bis-Tris, 30%(w/v) PEG3350, 4.5 mM Fe(NH4)2(SO4)2
Resolution 1.38 Å R-free 0.207
9KTE Co(II)-bound CpfC (HemH) Y13C variant modified with bromobimane Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C CO COBALT (II) ION × 6 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 3 9UM 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2, 0.1M Bis-Tris, 25%(w/v) PEG4000
Resolution 1.46 Å R-free 0.196
9KTF Ni(II)-bound Bacillus subtilis CpfC (HemH) Y13C variant modified with bromobimane Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C 9UM 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione × 1 MG MAGNESIUM ION × 3 NI NICKEL (II) ION × 2 CL CHLORIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2, 0.1M Bis-Tris, 25%(w/v) PEG4000, 4.5 mM NiCl2
Resolution 1.44 Å R-free 0.192
9KTG Cu(II)-bound CpfC (HemH) Y13C variant modified with bromobimane Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C 9UM 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione × 1 CU COPPER (II) ION × 5 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2, 0.1M Bis-Tris, 30%(w/v) PEG3350, 4.5 mM CuCl2
Resolution 1.44 Å R-free 0.197
9KTH Zn(II)-bound CpfC (HemH) Y13C variant modified with bromobimane Deposited 2024-12-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–310（310 aa）
Mutation：Y13C ZN ZINC ION × 6 MG MAGNESIUM ION × 3 9UM 3-(bromomethyl)-2,5,6-trimethyl-1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M MgCl2, 0.1M Bis-Tris, 30%(w/v) PEG3350
Resolution 1.90 Å R-free 0.247

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEMH_BACSU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–309； UniProt 2–310

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 3m4z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3m4z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3m4z
Deposition date deposition_date2010-03-12
Structure title titleCrystal Structure of B. subtilis ferrochelatase with Cobalt bound at the active site
Keywords keywordsCOBALT, METAL-BINDING, ROSSMANN FOLD, PI-HELIX, LYASE, Heme biosynthesis, Iron, Porphyrin biosynthesis; LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.20 Å
Radius of gyration Rg (electron density) rg_electron19.92 Å
Forward intensity I(0) i021605300.00
Molecular weight molecular_weight35352.0 kDa
Excluded volume excluded_volume44156 ų
Envelope volume envelope_volume51137 ų
Hydration-shell volume shell_volume21522 ų
Envelope diameter envelope_diameter68.5 Å
Shell Rg shell_rg26.43 Å
Envelope Rg envelope_rg20.17 Å
Shape Rg shape_rg19.90 Å
Total Rg total_rg20.85 Å
Total atoms total_atoms2489
Residues n_residues309
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 dmax67.8 Å
Rg (real space) rg_real21.12 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real2.1610e+07
I(0) uncertainty (real space) i0_real_error2.8890e+05
Rg (reciprocal space) rg_reciprocal21.14 Å
I(0) (reciprocal space) i0_reciprocal21610000.0000
Solution quality estimate total_estimate0.8971
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9 Å
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.325
Angular range angular_range— – 0.3750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4145000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3m4za_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.92 — Chelatase-like
Superfamily Superfamily superfamilyc.92.1 — Chelatase
Family Family familyc.92.1.1 — Ferrochelatase

CATH v4.4 (2 domains)

Domain ID domain_id3m4zA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1400 —
Domain ID domain_id3m4zA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1400 —
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8. Citations (1)

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9. Files and Curves (10)