3EEO | pdb_00003eeo

M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation.

PDB DOI: https://doi.org/10.2210/pdb3EEO/pdb
NAKB: 3EEO

Classification: TRANSFERASE/DNA
Organism(s): Haemophilus parahaemolyticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-05 Released: 2010-03-02
Deposition Author(s): Porta, J.C., Christman, J.K., Borgstahl, G.E.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.275 (Depositor)
R-Value Work:
0.237 (Depositor), 0.245 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation.

Porta, J.C., Christman, J.K., Borgstahl, G.E.O.

To be published.

Macromolecule Content

Total Structure Weight: 44.62 kDa
Atom Count: 3,226
Modeled Residue Count: 351
Deposited Residue Count: 351
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Modification methylase HhaI	C [auth A]	327	Haemophilus parahaemolyticus	Mutation(s): 0 Gene Names: hhaIM 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	Image
Entity ID: 1
5'-D(PDCPDCPDAPDTPDGPDCPDGPDCPDTPDGPDAPDC)-3'	A [auth C]	12	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
5'-D(PDGPDTPDCPDAPDGP(PDI)PDGPDCPDAPDTPDGPDG)-3'	B [auth D]	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM 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-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.275 (Depositor)
R-Value Work: 0.237 (Depositor), 0.245 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.479	α = 90
b = 95.479	β = 90
c = 318.353	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-02

Deposition Author(s):

Christman, J.K.

Borgstahl, G.E.O.

Revision History (Full details and data files)

Version 1.0: 2010-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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