5JLP | pdb_00005jlp

Crystal structure of Mycobacterium avium SerB2 in complex with serine at ACT domain

PDB DOI: https://doi.org/10.2210/pdb5JLP/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium avium 104
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-04-27 Released: 2017-05-03
Deposition Author(s): Shree, S., Ramachandran, R.
Funding Organization(s): CSIR

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.267 (Depositor), 0.269 (DCC)
R-Value Work:
0.191 (Depositor), 0.203 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Mycobacterium avium SerB2 in complex with serine at ACT domain

Shree, S., Ramachandran, R.

To be published.

Macromolecule Content

Total Structure Weight: 42.1 kDa
Atom Count: 2,849
Modeled Residue Count: 396
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine phosphatase	A	396	Mycobacterium avium 104	Mutation(s): 1 Gene Names: serB, MAV_3907 EC: 3.1.3.3
UniProt
Find proteins for A0QJI1 (Mycobacterium avium (strain 104)) Explore A0QJI1 Go to UniProtKB: A0QJI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QJI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.267 (Depositor), 0.269 (DCC)
R-Value Work: 0.191 (Depositor), 0.203 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.548	α = 90
b = 109.535	β = 90
c = 134.434	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-03

Deposition Author(s):

Ramachandran, R.

Funding Organization	Location	Grant Number
CSIR	India	--

Revision History (Full details and data files)

Version 1.0: 2017-05-03
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.