2UZ4 | pdb_00002uz4

HhaI DNA methyltransferase R165N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH

PDB DOI: https://doi.org/10.2210/pdb2UZ4/pdb
NAKB: 2UZ4

Classification: TRANSFERASE
Organism(s): Haemophilus parahaemolyticus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-25 Released: 2008-06-03
Deposition Author(s): Daujotyte, D., Leinartaite, L., Grazulis, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.210 (Depositor), 0.209 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

DNA Methyltransferase R165N Mutant

Daujotyte, D., Leinartaite, L., Grazulis, S.

To be published.

Macromolecule Content

Total Structure Weight: 45.6 kDa
Atom Count: 3,314
Modeled Residue Count: 352
Deposited Residue Count: 352
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MODIFICATION METHYLASE HHAI	A	327	Haemophilus parahaemolyticus	Mutation(s): 1 EC: 2.1.1.37
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus) Explore P05102 Go to UniProtKB: P05102
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05102
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5'-D(TPGPGPAPTPGP5CMPGPCPTPGP AP*C)-3'	B [auth C]	13	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
5'-D(GPTPCPAPGPCPGPCPAPTP CPC)-3'	C [auth D]	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	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 H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.235 (Depositor), 0.235 (DCC)
R-Value Work: 0.210 (Depositor), 0.209 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.177	α = 90
b = 95.177	β = 90
c = 312.355	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-06-03

Deposition Author(s):

Daujotyte, D.

Leinartaite, L.

Grazulis, S.

Revision History (Full details and data files)

Version 1.0: 2008-06-03
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description
Version 1.5: 2025-12-10
Changes: Data collection, Structure summary