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3wvp

Time-Resolved Crystal Structure of HindIII with 60sec soaking

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Type-2 restriction enzyme HindIII

Haemophilus influenzae

UniProt P43870

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') ; × 2 GLYCEROL × 2 MANGANESE (II) ION × 4 water × 4 Consistent with all polymers
2 Protein–DNA Homooligomer Protein 2 DNA 4 ;DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3') ; × 2 ;DNA (5'-D(*GP*CP*CP*A)-3') ; × 2 GLYCEROL × 2 MANGANESE (II) ION × 4 water × 6 Consistent with all polymers
3 Protein–DNA Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') ; × 2 GLYCEROL × 2 MANGANESE (II) ION × 4 water × 4 Consistent with all polymers
4 Protein–DNA Homooligomer Protein 2 DNA 4 ;DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3') ; × 2 ;DNA (5'-D(*GP*CP*CP*A)-3') ; × 2 GLYCEROL × 2 MANGANESE (II) ION × 4 water × 6 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2e52 2e52 3a4k 3a4k 3wvg 3wvg 3wvh 3wvh 3wvi 3wvi 3wvk 3wvk

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name T2D3_HAEIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–300； UniProt 1–300 Author chain B； PDBConstruct 1–300； UniProt 1–300 Author chain C； PDBConstruct 1–300； UniProt 1–300 Author chain D； PDBConstruct 1–300； UniProt 1–300

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_id3wvp
Deposition date deposition_date2014-06-02
Structure title titleTime-Resolved Crystal Structure of HindIII with 60sec soaking
Keywords keywordsFREEZE-TRAP, time-resolved, TYPE II RESTRICTION ENZYME, HYDROLASE, ENDONUCLEASE, nuclease, HYDROLASE-DNA complex; HYDROLASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3wvp__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3wvp__assembly_5__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3wvp__assembly_5__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）13.43 Å
Rg (electron density)12.97 Å
Total Rg13.72 Å
Atom count486
Residues24
Excluded volume7070 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3wvp__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3wvp__assembly_2__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3wvp__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3wvp__assembly_4__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3wvp__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3wvp__assembly_6__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3wvpA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily70 — Type II restriction endonuclease, HindIII
Domain ID domain_id3wvpA02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1510 —
Domain ID domain_id3wvpB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily70 — Type II restriction endonuclease, HindIII
Domain ID domain_id3wvpB02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1510 —
Domain ID domain_id3wvpC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily70 — Type II restriction endonuclease, HindIII
Domain ID domain_id3wvpC02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1510 —
Domain ID domain_id3wvpD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily70 — Type II restriction endonuclease, HindIII
Domain ID domain_id3wvpD02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1510 —
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7. Citations (1)