2BDE

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

PDB DOI: https://doi.org/10.2210/pdb2BDE/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Legionella pneumophila
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-10-20 Released: 2005-12-06
Deposition Author(s): Forouhar, F., Abashidze, M., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.267
R-Value Work: 0.221
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

Forouhar, F., Abashidze, M., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 55.35 kDa
Atom Count: 3,839
Modelled Residue Count: 458
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytosolic IMP-GMP specific 5'-nucleotidase	A	470	Legionella pneumophila	Mutation(s): 9 Gene Names: 3078646
UniProt
Find proteins for Q5ZZB6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZB6 Go to UniProtKB: Q5ZZB6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZZB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.267
R-Value Work: 0.221
R-Value Observed: 0.221
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.54	α = 90
b = 152.54	β = 90
c = 188.406	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-12-06

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-12-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description

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Help and Resources

2BDE

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)