3N58 | pdb_00003n58

Crystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form

PDB DOI: https://doi.org/10.2210/pdb3N58/pdb

Classification: HYDROLASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-24 Released: 2010-06-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.235 (Depositor), 0.233 (DCC)
R-Value Work:
0.172 (Depositor), 0.171 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form

SSGCID, Gardberg, A., Sankaran, B., Abendroth, J., Staker, B.

To be published.

Macromolecule Content

Total Structure Weight: 205.56 kDa
Atom Count: 14,819
Modeled Residue Count: 1,843
Deposited Residue Count: 1,856
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	464	Brucella abortus 2308	Mutation(s): 0 Gene Names: ahcY, BAB1_2099 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q2YQX8 (Brucella abortus (strain 2308)) Explore Q2YQX8 Go to UniProtKB: Q2YQX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YQX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], K [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
ADN Query on ADN Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], J [auth C], M [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth C] Focus chain M [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain E [auth A]	E [auth A], I [auth C], L [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.235 (Depositor), 0.233 (DCC)
R-Value Work: 0.172 (Depositor), 0.171 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.45	α = 90
b = 165.23	β = 90
c = 184.14	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2010-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2012-03-21
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

3N58 | pdb_00003n58

Crystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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