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1vhu

Crystal structure of a putative phosphoesterase

Method: X-RAY DIFFRACTION Dmax: 50.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hypothetical protein AF1521

Archaeoglobus fulgidus

UniProt O28751

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 2–199 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 experimental conditions Resolution 1.34 Å R-free 0.180

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 1VHU 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 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 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
2BFQ MACRO DOMAINS ARE ADP-RIBOSE BINDING MOLECULES Deposited 2004-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–192（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 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 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 4–201； UniProt 2–199

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 1vhu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vhu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vhu
Deposition date deposition_date2003-12-01
Structure title titleCrystal structure of a putative phosphoesterase
Keywords keywordsstructural genomics, unknown function; Structural genomics, unknown function
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_guinier16.85 Å
Radius of gyration Rg (electron density) rg_electron15.46 Å
Forward intensity I(0) i08168830.00
Molecular weight molecular_weight21310.0 kDa
Excluded volume excluded_volume26737 ų
Envelope volume envelope_volume29006 ų
Hydration-shell volume shell_volume15535 ų
Envelope diameter envelope_diameter49.0 Å
Shell Rg shell_rg21.62 Å
Envelope Rg envelope_rg15.66 Å
Shape Rg shape_rg15.41 Å
Total Rg total_rg16.65 Å
Total atoms total_atoms1480
Residues n_residues187
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 dmax50.5 Å
Rg (real space) rg_real16.71 Å
Rg uncertainty (real space) rg_real_error0.23 Å
I(0) (real space) i0_real8.1690e+06
I(0) uncertainty (real space) i0_real_error8.7170e+04
Rg (reciprocal space) rg_reciprocal16.73 Å
I(0) (reciprocal space) i0_reciprocal8169000.0000
Solution quality estimate total_estimate0.9050
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.031
Kurtosis Kurtosis kurtosis-0.497
Angular range angular_range— – 0.4700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2072000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.997
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1vhua_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.50 — Macro domain-like
Superfamily Superfamily superfamilyc.50.1 — Macro domain-like
Family Family familyc.50.1.2 — Macro domain

CATH v4.4 (1 domains)

Domain ID domain_id1vhuA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
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8. Citations (1)

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9. Files and Curves (10)