1AIH | pdb_00001aih

CATALYTIC DOMAIN OF BACTERIOPHAGE HP1 INTEGRASE

PDB DOI: https://doi.org/10.2210/pdb1AIH/pdb

Classification: DNA INTEGRATION
Organism(s): Hpunavirus HP1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1997-04-17 Released: 1997-08-20
Deposition Author(s): Hickman, A.B., Waninger, S., Scocca, J.J., Dyda, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.272 (Depositor)
R-Value Work:
0.209 (Depositor)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Molecular organization in site-specific recombination: the catalytic domain of bacteriophage HP1 integrase at 2.7 A resolution.

Hickman, A.B., Waninger, S., Scocca, J.J., Dyda, F.

(1997) Cell 89: 227-237

PubMed: 9108478 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(00)80202-0
Primary Citation Related Structures:
1AIH

PubMed Abstract:
HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenzae. The isolated C-terminal domain (residues 165-337) of the protein interacts with the recombination site and contains the four catalytic residues conserved in the integrase family. This domain represents a novel fold consisting principally of well-packed alpha helices, a surface beta sheet, and an ordered 17-residue C-terminal tail. The conserved triad of basic residues and the active-site tyrosine are contributed by a single monomer and occupy fixed positions in a defined active-site cleft. Dimers are formed by mutual interactions of the tail of one monomer with an adjacent monomer; this orients active-site clefts antiparallel to each other.

Organizational Affiliation

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecule Content

Total Structure Weight: 78.72 kDa
Atom Count: 5,545
Modeled Residue Count: 676
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HP1 INTEGRASE	A, B, C, D	170	Hpunavirus HP1	Mutation(s): 0 Gene Names: GENBANK U24159 EC: 3.1 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for P21442 (Haemophilus phage HP1 (strain HP1c1)) Explore P21442 Go to UniProtKB: P21442
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21442
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], M [auth C], N [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272 (Depositor)
R-Value Work: 0.209 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.4	α = 90
b = 129.3	β = 90
c = 234.2	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 1997-08-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1997-08-20
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations