2PH5 | pdb_00002ph5

Crystal structure of the homospermidine synthase hss from Legionella pneumophila in complex with NAD, Northeast Structural Genomics Target LgR54

PDB DOI: https://doi.org/10.2210/pdb2PH5/pdb

Classification: TRANSFERASE
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-10 Released: 2007-05-15
Deposition Author(s): Forouhar, F., Hussain, M., Seetharaman, J., Fang, Y., Janjua, H., Xiao, R., Cunningham, K., Ma, L.-C., Owens, L., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.261 (Depositor), 0.275 (DCC)
R-Value Work:
0.202 (Depositor), 0.218 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of the homospermidine synthase hss from Legionella pneumophila in complex with NAD.

Forouhar, F., Hussain, M., Seetharaman, J., Fang, Y., Janjua, H., Xiao, R., Cunningham, K., Ma, L.-C., Owens, L., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 55.19 kDa
Atom Count: 3,856
Modeled Residue Count: 459
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homospermidine synthase	A	480	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 8 Gene Names: hss, lpg2495 EC: 2.5.1.44
UniProt
Find proteins for Q5ZSM2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSM2 Go to UniProtKB: Q5ZSM2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZSM2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 2.50 Å
R-Value Free: 0.261 (Depositor), 0.275 (DCC)
R-Value Work: 0.202 (Depositor), 0.218 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.848	α = 90
b = 146.902	β = 90
c = 85.685	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-05-15
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
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary