SAXSdb — 6l2d

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

Cupin_2 domain-containing protein

Thermotoga maritima MSB8

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 1–114 Chain B； UniProt 1–114	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1M MES	Resolution 1.20 Å R-free 0.186

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 6L2D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1VJ2 Crystal structure of a novel family of manganese-containing cupin (tm1459) from thermotoga maritima at 1.65 A resolution Deposited 2003-12-03	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 1–114（114 aa） Chain B 1–114（114 aa）	Not recorded	MN MANGANESE (II) ION × 2 UNL UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION,SITTING DROP,NANODROP；pH 5.2；293 K；50% (v/v) PEG-200, 0.1M Phosphate-citrate pH 4.2 0.2M NaCl, pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K	Resolution 1.65 Å R-free 0.249
5WSD Crystal structure of a cupin protein (tm1459) in apo form Deposited 2016-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain B 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% Jeffamine ED-2001, 0.1M MES	Resolution 1.20 Å R-free 0.201
5WSE Crystal structure of a cupin protein (tm1459) in osmium (Os) substituted form I Deposited 2016-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain D 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES	Resolution 1.12 Å R-free 0.180
5WSE Crystal structure of a cupin protein (tm1459) in osmium (Os) substituted form I Deposited 2016-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–114（114 aa） Chain C 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES	Resolution 1.12 Å R-free 0.180
5WSF Crystal structure of a cupin protein (tm1459) in osmium (Os)-substituted form II Deposited 2016-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain D 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES	Resolution 1.11 Å R-free 0.183
5WSF Crystal structure of a cupin protein (tm1459) in osmium (Os)-substituted form II Deposited 2016-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–114（114 aa） Chain C 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% w/v polyethylene glycol 1500, 0.1M MES	Resolution 1.11 Å R-free 0.183
6L2E Crystal structure of a cupin protein (tm1459, H52A mutant) in copper (Cu) substituted form Deposited 2019-10-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain B 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES	Resolution 1.20 Å R-free 0.179
6L2F Crystal structure of a cupin protein (tm1459, H54AH58A mutant) in copper (Cu) substituted form Deposited 2019-10-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain B 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1M MES	Resolution 1.23 Å R-free 0.188
8AWN Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant C106Q Deposited 2022-08-30	Different construct 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 1–114（114 aa）	Mutation：C106Q	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；289 K；1 M LiCl 0.1 M citrate pH 4.0 20 % PEG6000 16 mg/ml protein concentration	Resolution 1.45 Å R-free 0.173
8AWO Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant AIFQ (Y7A/M38I/Y83F/C106Q) Deposited 2022-08-30	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：Y7A, M38I, Y83F, C106Q Mutation：Y7A, M38I, Y83F, C106Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；8 mg/ml protein concentration 0.1 M Tris pH 8.5 2 M ammonium sulfate	Resolution 1.70 Å R-free 0.242
8AWP Crystal structure of a manganese-containing cupin (tm1459) from Thermotoga maritima, variant 208 (V19I/R23H/M38I/I60F/C106Q) Deposited 2022-08-30	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：V19I, R23H, M38I, I60F, C106Q Mutation：V19I, R23H, M38I, I60F, C106Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；14.2 mg/ml protein concentration 1.6M Sodium citrate tribasic dihydrate pH 6.5	Resolution 1.59 Å R-free 0.208
8HJX Crystal structure of a cupin protein (tm1459, H52A/H58E mutant) in copper (Cu) substituted form Deposited 2022-11-24	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：H52A/H58E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H52A/H58E Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% w/v Jeffamine ED-2001, 0.1M MES pH6.0	Resolution 1.15 Å R-free 0.183
8HJY Crystal structure of a cupin protein (tm1459, H52A/H58E/F104W mutant) in copper (Cu) substituted form Deposited 2022-11-24	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：H52A/H58E/F104W Mutation：H52A/H58E/F104W	CU COPPER (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% w/v Jeffamine ED-2001, 0.1M MES pH 6.0	Resolution 1.18 Å R-free 0.191
8HJZ Crystal structure of a cupin protein (tm1459, H52A/H58Q mutant) in copper (Cu) substituted form Deposited 2022-11-24	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：H52A/H58Q Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H52A/H58Q Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% w/v Jeffamine ED-2001, 0.1M MES pH 6.0	Resolution 1.22 Å R-free 0.188
8ZYG Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/C106D mutant) in copper (Cu) substituted form Deposited 2024-06-17	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：I49C/H52A/C106D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I49C/H52A/C106D Non-standard monomer：Yes (specific site not provided by mmCIF)	P6G HEXAETHYLENE GLYCOL × 1 CU COPPER (II) ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；26-28% w/v Jeffamine ED-2001, 0.1M MES pH6.0	Resolution 1.08 Å R-free 0.171
8ZYH Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/H54A/C106D mutant) in copper (Cu) substituted form Deposited 2024-06-17	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：I49C/H52A/H54A/C106D Mutation：I49C/H52A/H54A/C106D	P6G HEXAETHYLENE GLYCOL × 1 CU COPPER (II) ION × 3 KN6 4-THIOPYRIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；26-28% w/v Jeffamine ED-2001, 0.1M MES pH6.0	Resolution 1.07 Å R-free 0.163
9JET Crystal structure of a cupin protein (tm1459) in manganese (Mn) substituted form Deposited 2024-09-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain B 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1M MES	Resolution 1.19 Å R-free 0.201
9JEU Crystal structure of a cupin protein (tm1459) in iron (Fe) substituted form Deposited 2024-09-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain B 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1 M MES	Resolution 1.19 Å R-free 0.186
9JEV Crystal structure of a cupin protein (tm1459) in zinc (Zn) substituted form Deposited 2024-09-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Chain B 1–114（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1 M MES	Resolution 1.12 Å R-free 0.177
9JEW Crystal structure of a cupin protein (tm1459, C106V mutant) in iron (Fe) substituted form Deposited 2024-09-03	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：C106V Mutation：C106V	FE FE (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25%(w/v) Jeffamine ED-2001, 0.1 M MES	Resolution 1.08 Å R-free 0.168
9XS8 Crystal structure of a cupin protein (tm1459, H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form Deposited 2025-11-20	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：H52A/H54A/H92A/C106E Mutation：H52A/H54A/H92A/C106E	MML 1-methyl-4-(1-methylethyl)benzene × 1 RU RUTHENIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES	Resolution 1.26 Å R-free 0.198
9XS9 Crystal structure of a cupin protein (tm1459, R39K/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form Deposited 2025-11-20	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：R39K/H52A/H54A/H92A/C106E Mutation：R39K/H52A/H54A/H92A/C106E	MML 1-methyl-4-(1-methylethyl)benzene × 2 RU RUTHENIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES	Resolution 1.09 Å R-free 0.161
9XSA Crystal structure of a cupin protein (tm1459, R39M/H52A/H54A/H92A/C106E mutant) in ruthenium(p-cymene) bound form Deposited 2025-11-20	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 1–114（114 aa） Chain B 1–114（114 aa）	Mutation：R39M/H52A/H54A/H92A/C106E Mutation：R39M/H52A/H54A/H92A/C106E	MML 1-methyl-4-(1-methylethyl)benzene × 2 RU RUTHENIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；25% w/v Jeffamine ED-2001, 0.1M MES	Resolution 1.42 Å R-free 0.251

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

View Construct and Data Evidence

UniProt name	Q9X1H0_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–118； UniProt 1–114 Author chain B； PDBConstruct 5–118； UniProt 1–114

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6l2d
Deposition date deposition_date	2019-10-03
Structure title title	Crystal structure of a cupin protein (tm1459) in copper (Cu) substituted form
Keywords keywords	Artificial metalloenzymes, Copper enzyme, Cupin, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	18.65 Å
Radius of gyration Rg (electron density) rg_electron	17.20 Å
Forward intensity I(0) i0	11981000.00
Molecular weight molecular_weight	26139.0 kDa
Excluded volume excluded_volume	32818 Å³
Envelope volume envelope_volume	36571 Å³
Hydration-shell volume shell_volume	17717 Å³
Envelope diameter envelope_diameter	59.9 Å
Shell Rg shell_rg	23.49 Å
Envelope Rg envelope_rg	17.46 Å
Shape Rg shape_rg	17.19 Å
Total Rg total_rg	18.19 Å
Total atoms total_atoms	3639
Residues n_residues	230
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	60.1 Å
Rg (real space) rg_real	18.56 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.1980e+07
I(0) uncertainty (real space) i0_real_error	1.5790e+05
Rg (reciprocal space) rg_reciprocal	18.57 Å
I(0) (reciprocal space) i0_reciprocal	11980000.0000
Solution quality estimate total_estimate	0.7063
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	59.2 Å
Skewness Skewness skewness	0.214
Kurtosis Kurtosis kurtosis	-0.367
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2516000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 0.197; Positv: 1.000; Valcen: 0.998; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cupin_2 domain-containing protein
Molecular weight formula_weight	13459.4 kDa
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	3997

GPSGMILKRAYDVTPQKISTDKVRGVRKRVLIGLKDAPNFVMRLFTVEPGGLIDRHSHPWEHEIFVLKGKLTVLKEQGEETVEEGFYIFVEPNEIHGFRNDTDSEVEFLCLIPKEGGE

来源 Source

来源生物 organism	Thermotoga maritima MSB8
NCBI Class编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6l2da1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.10 — TM1459-like

Domain ID domain_id	d6l2da2
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	d6l2db_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.10 — TM1459-like

CATH v4.4 (2 domains)

Domain ID domain_id	6l2dA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	6l2dB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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8. Citations (1)

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Unit-cell length a length_a	50.521 Å
Unit-cell length b length_b	57.808 Å
Unit-cell length c length_c	74.963 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.198 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1508
R_work r_work	0.1508
R_free r_free	0.1857

fit	/app/data/saxs_computation/l2/6l2d/6l2d.fit
pddf	/app/data/pr_computation/l2/6l2d/6l2d.pr.out
profile	/app/data/saxs_computation/l2/6l2d/6l2d.dat

Crystal structure of a cupin protein (tm1459) in copper (Cu) substituted form

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

Cupin_2 domain-containing protein

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