1d5n

CRYSTAL STRUCTURE OF E. COLI MNSOD AT 100K

Method: X-RAY DIFFRACTION D_max: 112.6 Å Quality: GOOD

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

PROTEIN (MANGANESE SUPEROXIDE DISMUTASE)

OrganismNot specified

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–205 Chain B； UniProt 1–205	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.50	Resolution 1.55 Å R-free 0.233
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–205 Chain D； UniProt 1–205	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.50	Resolution 1.55 Å R-free 0.233

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 1D5N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EN4 CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Q146H MUTANT Deposited 2000-03-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：Q146H Mutation：Q146H	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；20% w/v PEG 6000, 0.05 M bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.192
1EN4 CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Q146H MUTANT Deposited 2000-03-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–205（205 aa） Chain D 1–205（205 aa）	Mutation：Q146H Mutation：Q146H	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；20% w/v PEG 6000, 0.05 M bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.192
1EN5 CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Y34F MUTANT Deposited 2000-03-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：Y34F Mutation：Y34F	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；298 K；20% w/v PEG 6000, 0.1 M bicine, 25 mM sodium azide, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.195
1EN5 CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Y34F MUTANT Deposited 2000-03-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–205（205 aa） Chain D 1–205（205 aa）	Mutation：Y34F Mutation：Y34F	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；298 K；20% w/v PEG 6000, 0.1 M bicine, 25 mM sodium azide, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.30 Å R-free 0.195
1EN6 CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Q146L MUTANT Deposited 2000-03-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：Q146L Mutation：Q146L	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；20% w/v PEG 6000, 0.05 M bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.207
1EN6 CRYSTAL STRUCTURE ANALYSIS OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE Q146L MUTANT Deposited 2000-03-20	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–205（205 aa） Chain D 1–205（205 aa）	Mutation：Q146L Mutation：Q146L	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；20% w/v PEG 6000, 0.05 M bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.207
1I08 CRYSTAL STRUCTURE ANALYSIS OF THE H30A MUTANT OF MANGANESE SUPEROXIDE DISMUTASE FROM E. COLI Deposited 2001-01-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：H30A Mutation：H30A	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；16-20% PEG 6000, 0.1 M bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.211
1I08 CRYSTAL STRUCTURE ANALYSIS OF THE H30A MUTANT OF MANGANESE SUPEROXIDE DISMUTASE FROM E. COLI Deposited 2001-01-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–205（205 aa） Chain D 1–205（205 aa）	Mutation：H30A Mutation：H30A	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；16-20% PEG 6000, 0.1 M bicine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.211
1I0H CRYSTAL STRUCTURE OF THE E. COLI MANGANESE SUPEROXIDE DISMUTASE MUTANT Y174F AT 1.35 ANGSTROMS RESOLUTION. Deposited 2001-01-29	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：Y174F Mutation：Y174F	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；16-20% PEG 6000, 0.1M bicine ph 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.35 Å R-free 0.196
1IX9 Crystal Structure of the E. coli Manganase(III) superoxide dismutase mutant Y174F at 0.90 angstroms resolution. Deposited 2002-06-17	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：Y174F Mutation：Y174F	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；16-20% PEG6000, 0.1M BICINE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 0.90 Å R-free 0.127
1IXB CRYSTAL STRUCTURE OF THE E. COLI MANGANESE(II) SUPEROXIDE DISMUTASE MUTANT Y174F AT 0.90 ANGSTROMS RESOLUTION. Deposited 2002-06-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：Y174F Mutation：Y174F	MH2 MANGANESE ION, 1 HYDROXYL COORDINATED × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；16-20% PEG6000, 0.1M BICINE. CRYSTALS WERE REDUCED JUST PRIOR TO FREEZING BY ADDITION OF 10% H2O2 (1 PART to 40 PARTS MOTHER LIQUOR), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 0.90 Å R-free 0.126
1MMM DISTINCT METAL ENVIRONMENT IN IRON-SUBSTITUTED MANGANESE SUPEROXIDE DISMUTASE PROVIDES A STRUCTURAL BASIS OF METAL SPECIFICITY Deposited 1998-08-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Not recorded	OH HYDROXIDE ION × 3 FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.75；pH 8.75	Resolution 2.20 Å R-free 0.231
1VEW MANGANESE SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI Deposited 1998-01-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Not recorded	MN MANGANESE (II) ION × 2 OH HYDROXIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING DROP METHOD. THE HANGING DROPS WERE SUSPENDED OVER 0.75ML OF WELL SOLUTION (16-30% PEG6000 AND 0.05M BICINE TITRATED TO PH8.5) AND CONSISTED OF 2UL OF WELL SOLUTION AND 2UL OF PROTEIN SOLUTION (MNSOD AT 12MG/ML IN WATER)., vapor diffusion - hanging drop	Resolution 2.10 Å R-free 0.210
1VEW MANGANESE SUPEROXIDE DISMUTASE FROM ESCHERICHIA COLI Deposited 1998-01-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–205（205 aa） Chain D 1–205（205 aa）	Not recorded	MN MANGANESE (II) ION × 2 OH HYDROXIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING DROP METHOD. THE HANGING DROPS WERE SUSPENDED OVER 0.75ML OF WELL SOLUTION (16-30% PEG6000 AND 0.05M BICINE TITRATED TO PH8.5) AND CONSISTED OF 2UL OF WELL SOLUTION AND 2UL OF PROTEIN SOLUTION (MNSOD AT 12MG/ML IN WATER)., vapor diffusion - hanging drop	Resolution 2.10 Å R-free 0.210
1ZLZ Re-Evaluation of the Low-Temperature Azide in Mn-Dependent Superoxide Dismutase Deposited 2005-05-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–205（205 aa） Chain B 1–205（205 aa）	Mutation：Y174F Mutation：Y174F	AZI AZIDE ION × 2 MH2 MANGANESE ION, 1 HYDROXYL COORDINATED × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；PEG 6000, MPD, TRIS buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.55 Å R-free 0.222
3K9S Crystal structure of the peroxide-bound manganese superoxide dismutase. Deposited 2009-10-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–206（205 aa） Chain B 2–206（205 aa）	Not recorded	MN MANGANESE (II) ION × 2 PEO HYDROGEN PEROXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；50 mM Bicine pH 8.5, 25% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.270
3K9S Crystal structure of the peroxide-bound manganese superoxide dismutase. Deposited 2009-10-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–206（205 aa） Chain D 2–206（205 aa）	Not recorded	MN MANGANESE (II) ION × 2 PEO HYDROGEN PEROXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；50 mM Bicine pH 8.5, 25% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.270
3OT7 Escherichia coli apo-manganese superoxide dismutase Deposited 2010-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–206（205 aa） Chain B 2–206（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；20% PEG 6000, 0.1M Bicine, 1mM EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.236
3OT7 Escherichia coli apo-manganese superoxide dismutase Deposited 2010-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–206（205 aa） Chain D 2–206（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；20% PEG 6000, 0.1M Bicine, 1mM EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.236

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

View Construct and Data Evidence

UniProt name	SODM_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–205； UniProt 1–205 Author chain B； PDBConstruct 1–205； UniProt 1–205 Author chain C； PDBConstruct 1–205； UniProt 1–205 Author chain D； PDBConstruct 1–205； UniProt 1–205

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d5n
Deposition date deposition_date	1999-10-08
Structure title title	CRYSTAL STRUCTURE OF E. COLI MNSOD AT 100K
Keywords keywords	MANGANESE SUPEROXIDE DISMUTASE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	33.23 Å
Radius of gyration Rg (electron density) rg_electron	32.99 Å
Forward intensity I(0) i0	130440000.00
Molecular weight molecular_weight	92076.0 kDa
Excluded volume excluded_volume	115420 Å³
Envelope volume envelope_volume	146900 Å³
Hydration-shell volume shell_volume	38102 Å³
Envelope diameter envelope_diameter	115.3 Å
Shell Rg shell_rg	38.87 Å
Envelope Rg envelope_rg	32.24 Å
Shape Rg shape_rg	32.99 Å
Total Rg total_rg	33.47 Å
Total atoms total_atoms	6516
Residues n_residues	820
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	112.6 Å
Rg (real space) rg_real	33.35 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	1.3040e+08
I(0) uncertainty (real space) i0_real_error	2.1230e+06
Rg (reciprocal space) rg_reciprocal	33.30 Å
I(0) (reciprocal space) i0_reciprocal	130400000.0000
Solution quality estimate total_estimate	0.8747
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.374
Kurtosis Kurtosis kurtosis	-0.439
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24940000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.865

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1d5na1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d1d5na2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

Domain ID domain_id	d1d5nb1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d1d5nb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

Domain ID domain_id	d1d5nc1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d1d5nc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

Domain ID domain_id	d1d5nd1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.11 — Fe,Mn superoxide dismutase (SOD), N-terminal domain
Family Family family	a.2.11.1 — Fe,Mn superoxide dismutase (SOD), N-terminal domain

Domain ID domain_id	d1d5nd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.44 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Superfamily Superfamily superfamily	d.44.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain
Family Family family	d.44.1.1 — Fe,Mn superoxide dismutase (SOD), C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1d5nA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

Domain ID domain_id	1d5nA02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

Domain ID domain_id	1d5nB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

Domain ID domain_id	1d5nB02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

Domain ID domain_id	1d5nC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

Domain ID domain_id	1d5nC02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

Domain ID domain_id	1d5nD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	990 — Fe,Mn superoxide dismutase (SOD) domain

Domain ID domain_id	1d5nD02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	40 — minor pseudopilin epsh fold
Homologous superfamily homologous superfamily	20 — Iron/manganese superoxide dismutase, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	99.110 Å
Unit-cell length b length_b	107.300 Å
Unit-cell length c length_c	179.110 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2330

Description description	PROTEIN (MANGANESE SUPEROXIDE DISMUTASE)
Molecular weight formula_weight	22996.9 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	nat
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7672

CRYSTAL STRUCTURE OF E. COLI MNSOD AT 100K

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

PROTEIN (MANGANESE SUPEROXIDE DISMUTASE)

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1085

fit	/app/data/saxs_computation/d5/1d5n/1d5n.fit
pddf	/app/data/pr_computation/d5/1d5n/1d5n.pr.out
profile	/app/data/saxs_computation/d5/1d5n/1d5n.dat