2QLT | pdb_00002qlt

Crystal structure of an isoform of DL-glycerol-3-phosphatase, Rhr2p, from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb2QLT/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-07-13 Released: 2007-08-07
Deposition Author(s): Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.195 (Depositor), 0.194 (DCC)
R-Value Work:
0.168 (Depositor), 0.167 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of an isoform of DL-glycerol-3-phosphatase, Rhr2p from Saccharomyces cerevisiae.

Tan, K., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.21 kDa
Atom Count: 2,307
Modeled Residue Count: 251
Deposited Residue Count: 275
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(DL)-glycerol-3-phosphatase 1	A	275	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: GPP1, RHR2, YIL053W EC: 3.1.3 (PDB Primary Data), 3.1.3.21 (UniProt)
UniProt
Find proteins for P41277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41277 Go to UniProtKB: P41277
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41277
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.195 (Depositor), 0.194 (DCC)
R-Value Work: 0.168 (Depositor), 0.167 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.636	α = 90
b = 55.578	β = 90
c = 97.748	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-08-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-08-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations