3E5Z | pdb_00003e5z

X-Ray structure of the putative gluconolactonase in protein family PF08450. Northeast Structural Genomics Consortium target DrR130.

PDB DOI: https://doi.org/10.2210/pdb3E5Z/pdb

Classification: structural genomics, unknown function
Organism(s): Deinococcus radiodurans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-14 Released: 2008-09-30
Deposition Author(s): Kuzin, A.P., Abashidze, M., Seetharaman, J., Wang, D., Mao, L., Maglaqui, M., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Tong, S.N., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.229 (Depositor), 0.232 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

X-Ray structure of the putative gluconolactonase in protein family PF08450. Northeast Structural Genomics Consortium target DrR130.

Kuzin, A.P., Abashidze, M., Seetharaman, J., Wang, D., Mao, L., Maglaqui, M., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Tong, S.N., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 65.79 kDa
Atom Count: 4,731
Modeled Residue Count: 580
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Gluconolactonase	A, B	296	Deinococcus radiodurans	Mutation(s): 0 Gene Names: DR_0277
UniProt
Find proteins for Q9RXN3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RXN3 Go to UniProtKB: Q9RXN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RXN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.229 (Depositor), 0.232 (DCC)
R-Value Work: 0.193 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.42	α = 90
b = 93.4	β = 98.67
c = 76.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-09-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary