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1c3r

CRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH TRICHOSTATIN A

Method: X-RAY DIFFRACTION Dmax: 87.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HDLP (HISTONE DEACETYLASE-LIKE PROTEIN)

Aquifex aeolicus

UniProt O67135

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 1–375 Chain B； UniProt 1–375 Mutation：C75S, C77S ZN ZINC ION × 2 TSN TRICHOSTATIN A × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.00 Å R-free 0.258

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 1C3R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C3P CRYSTAL STRUCTURE OF AN HDAC HOMOLOG FROM AQUIFEX AEOLICUS Deposited 1999-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–375（375 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PEG 1500, SODIUM CHLORIDE, ISOPROPANOL, TRIS-HCL, pH 7.00
Resolution 1.80 Å R-free 0.240

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O67135_AQUAE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–375； UniProt 1–375 Author chain B； PDBConstruct 1–375； UniProt 1–375

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 1c3r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c3r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1c3r
Deposition date deposition_date1999-07-28
Structure title titleCRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH TRICHOSTATIN A
Keywords keywordsALPHA/BETA FOLD, HYDROXAMIC ACID, CHARGE-RELAY SYSTEM, PENTA-COORDINATED ZINC, LYASE; LYASE
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_guinier28.04 Å
Radius of gyration Rg (electron density) rg_electron27.37 Å
Forward intensity I(0) i0108384000.00
Molecular weight molecular_weight85248.0 kDa
Excluded volume excluded_volume107920 ų
Envelope volume envelope_volume124140 ų
Hydration-shell volume shell_volume36971 ų
Envelope diameter envelope_diameter93.5 Å
Shell Rg shell_rg35.41 Å
Envelope Rg envelope_rg27.32 Å
Shape Rg shape_rg27.31 Å
Total Rg total_rg28.34 Å
Total atoms total_atoms6024
Residues n_residues744
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 dmax87.0 Å
Rg (real space) rg_real27.96 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real1.0840e+08
I(0) uncertainty (real space) i0_real_error1.5260e+06
Rg (reciprocal space) rg_reciprocal27.99 Å
I(0) (reciprocal space) i0_reciprocal108400000.0000
Solution quality estimate total_estimate0.9011
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.0 Å
Skewness Skewness skewness0.289
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33280000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.918
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1c3ra_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.2 — Histone deacetylase, HDAC
Domain ID domain_idd1c3rb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.2 — Histone deacetylase, HDAC

CATH v4.4 (2 domains)

Domain ID domain_id1c3rA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
Domain ID domain_id1c3rB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily20 — Histone deacetylase domain
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8. Citations (1)

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9. Files and Curves (10)