SAXSdb — 6fx7

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

[Protein ADP-ribosylglutamate] hydrolase AF_1521

Archaeoglobus fulgidus DSM 4304

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 1–192	Mutation：K15R, K35E, Y74C, F97L, I103V, S105G, E110G, Y145R, N162D	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25 %w/v PEG3350, 0,2M sodium chloride, 0.1 M bis-tris, 2mM ADP-ribose	Resolution 1.82 Å R-free 0.212

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 6FX7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HJZ Crystal structure of AF1521 protein containing a macroH2A domain Deposited 2003-03-05	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 1–192（192 aa） Fragment：MACROH2A	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES BUFFER, PH 6.5 18% PEG 5000 MME, 0.2M AMMONIUM SULPHATE, 25MM MANGANESE CHLORIDE	Resolution 1.70 Å R-free 0.227
1HJZ Crystal structure of AF1521 protein containing a macroH2A domain Deposited 2003-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–192（192 aa） Fragment：MACROH2A	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1M MES BUFFER, PH 6.5 18% PEG 5000 MME, 0.2M AMMONIUM SULPHATE, 25MM MANGANESE CHLORIDE	Resolution 1.70 Å R-free 0.227
1VHU Crystal structure of a putative phosphoesterase Deposited 2003-12-01	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 2–199（198 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.34 Å R-free 0.180
2BFQ MACRO DOMAINS ARE ADP-RIBOSE BINDING MOLECULES Deposited 2004-12-10	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–192（192 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；30% PEG 4000, 0.2 AMMONIUM ACETATE, 0.1 TRI SODIUM CITRATE (PH 5.6), 18MG/ML PROTEIN, 1.5 MM ADP-RIBOSE, 5MM DTT. CRYO BUFFER CONTAINED 20% GLYCEROL	Resolution 1.50 Å R-free 0.233
2BFR The Macro domain is an ADP-ribose binding module Deposited 2004-12-10	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 1–192（192 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；20% PEG 8000, 0.2 MAGNESIUM ACETATE, 0.1M SODIUM CACODYLATE (PH 4.5). 18MG/ML PROTEIN, 1.5MM ADP, 5MM DTT. CRYOBUFFER CONTAINED 20% GLYCEROL.	Resolution 2.50 Å R-free 0.237
7WR6 Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521 Deposited 2022-01-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–192（192 aa）	Not recorded	5ZY [[(3~{a}~{S},5~{R},6~{R},6~{a}~{R})-2-azanylidene-3-[(4~{R})-4-azanyl-5-oxidanylidene-pentyl]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxazol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；27% PEG 3350, 0.05M CAPSO pH 9.0	Resolution 1.96 Å R-free 0.228

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Y1521_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–215； UniProt 1–192

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	6fx7
Deposition date deposition_date	2018-03-08
Structure title title	Crystal structure of in vitro evolved Af1521
Keywords keywords	Macro domain, ADP-ribose binding, SIGNALING PROTEIN; SIGNALING 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	16.77 Å
Radius of gyration Rg (electron density) rg_electron	15.47 Å
Forward intensity I(0) i0	8577820.00
Molecular weight molecular_weight	21590.0 kDa
Excluded volume excluded_volume	27048 Å³
Envelope volume envelope_volume	29726 Å³
Hydration-shell volume shell_volume	15796 Å³
Envelope diameter envelope_diameter	50.0 Å
Shell Rg shell_rg	21.83 Å
Envelope Rg envelope_rg	15.78 Å
Shape Rg shape_rg	15.44 Å
Total Rg total_rg	16.61 Å
Total atoms total_atoms	1512
Residues n_residues	193
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	51.5 Å
Rg (real space) rg_real	16.64 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	8.5780e+06
I(0) uncertainty (real space) i0_real_error	8.7590e+04
Rg (reciprocal space) rg_reciprocal	16.66 Å
I(0) (reciprocal space) i0_reciprocal	8578000.0000
Solution quality estimate total_estimate	0.8977
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.054
Kurtosis Kurtosis kurtosis	-0.455
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2284000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.999

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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	[Protein ADP-ribosylglutamate] hydrolase AF_1521
Molecular weight formula_weight	23575.9 kDa
EC 编号 ec_number	3.2.2.-
Mutation mutation	K15R, K35E, Y74C, F97L, I103V, S105G, E110G, Y145R, N162D
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1642

MGHHHHHHHHHHSSGHIDDDDKHMEVLFEAKVGDITLRLAQGDITQYPAKAIVNAANERLEHGGGVAYAIAKACAGDAGLYTEISKKAMREQFGRDCIDHGEVVVTPAMNLEERGIKYVLHTVGPVCGGMWSGELKEKLYKAFLGPLEKAEEMGVESIAFPAVSAGIRGCDLEKVVETFLEAVKDFKGSAVKEVALVIYDRKSAEVALKVFERSL

来源 Source

来源生物 organism	Archaeoglobus fulgidus DSM 4304
NCBI Class编号 ncbi_taxonomy_id	224325
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6fx7a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.50 — Macro domain-like
Superfamily Superfamily superfamily	c.50.1 — Macro domain-like
Family Family family	c.50.1.2 — Macro domain

Domain ID domain_id	d6fx7a2
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 (1 domains)

Domain ID domain_id	6fx7A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

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8. Citations (1)

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Unit-cell length a length_a	141.312 Å
Unit-cell length b length_b	39.535 Å
Unit-cell length c length_c	35.964 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	70.020 Å
R factor r_factor	0.1880
R_work r_work	0.1870
R_free r_free	0.2120

fit	/app/data/saxs_computation/fx/6fx7/6fx7.fit
pddf	/app/data/pr_computation/fx/6fx7/6fx7.pr.out
profile	/app/data/saxs_computation/fx/6fx7/6fx7.dat

Crystal structure of in vitro evolved Af1521

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

[Protein ADP-ribosylglutamate] hydrolase AF_1521

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