SAXSdb — 1hjz

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

HYPOTHETICAL PROTEIN AF1521

ARCHAEOGLOBUS FULGIDUS

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	Fragment：MACROH2A	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–192	Fragment：MACROH2A	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

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 1HJZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1VHU Crystal structure of a putative phosphoesterase Deposited 2003-12-01	Different construct Different mutation/modification 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 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）	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 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）	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
6FX7 Crystal structure of in vitro evolved Af1521 Deposited 2018-03-08	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）	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
7WR6 Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521 Deposited 2022-01-26	Different construct 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YF21_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–192； UniProt 1–192 Author chain B； PDBConstruct 1–192； 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	1hjz
Deposition date deposition_date	2003-03-05
Structure title title	Crystal structure of AF1521 protein containing a macroH2A domain
Keywords keywords	MACRO_H2A DOMAIN/HYDROLASE, HISTONE MACROH2A, CRYSTAL STRUCTURE P-LOOP NUCLEOTIDE HYDROLASE, MACRO_H2A DOMAIN-HYDROLASE complex; MACRO_H2A DOMAIN/HYDROLASE
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	26.28 Å
Radius of gyration Rg (electron density) rg_electron	25.55 Å
Forward intensity I(0) i0	28170500.00
Molecular weight molecular_weight	42295.0 kDa
Excluded volume excluded_volume	53566 Å³
Envelope volume envelope_volume	64663 Å³
Hydration-shell volume shell_volume	21666 Å³
Envelope diameter envelope_diameter	84.5 Å
Shell Rg shell_rg	32.06 Å
Envelope Rg envelope_rg	25.26 Å
Shape Rg shape_rg	25.53 Å
Total Rg total_rg	26.39 Å
Total atoms total_atoms	2970
Residues n_residues	384
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	80.7 Å
Rg (real space) rg_real	26.38 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	2.8170e+07
I(0) uncertainty (real space) i0_real_error	3.9220e+05
Rg (reciprocal space) rg_reciprocal	26.35 Å
I(0) (reciprocal space) i0_reciprocal	28170000.0000
Solution quality estimate total_estimate	0.8739
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.333
Kurtosis Kurtosis kurtosis	-0.706
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4166000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.787

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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	HYPOTHETICAL PROTEIN AF1521
Molecular weight formula_weight	20983.2 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	3249

MEVLFEAKVGDITLKLAQGDITQYPAKAIVNAANKRLEHGGGVAYAIAKACAGDAGLYTEISKKAMREQFGRDYIDHGEVVVTPAMNLEERGIKYVFHTVGPICSGMWSEELKEKLYKAFLGPLEKAEEMGVESIAFPAVSAGIYGCDLEKVVETFLEAVKNFKGSAVKEVALVIYDRKSAEVALKVFERSL

来源 Source

来源生物 organism	ARCHAEOGLOBUS FULGIDUS
NCBI Class编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 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	279

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1hjza_
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	d1hjzb_
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

CATH v4.4 (2 domains)

Domain ID domain_id	1hjzA00
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

Domain ID domain_id	1hjzB00
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	119.930 Å
Unit-cell length b length_b	55.720 Å
Unit-cell length c length_c	62.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2270

fit	/app/data/saxs_computation/hj/1hjz/1hjz.fit
pddf	/app/data/pr_computation/hj/1hjz/1hjz.pr.out
profile	/app/data/saxs_computation/hj/1hjz/1hjz.dat

Crystal structure of AF1521 protein containing a macroH2A domain

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

HYPOTHETICAL PROTEIN AF1521

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