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- PDB-2ph5: Crystal structure of the homospermidine synthase hss from Legione... -

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Basic information

Entry
Database: PDB / ID: 2ph5
TitleCrystal structure of the homospermidine synthase hss from Legionella pneumophila in complex with NAD, Northeast Structural Genomics Target LgR54
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


homospermidine synthase / homospermidine synthase activity / membrane => GO:0016020 / oxidoreductase activity / nucleotide binding
Similarity search - Function
homospermidine synthase like / Homospermidine synthase-like, C-terminal / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...homospermidine synthase like / Homospermidine synthase-like, C-terminal / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsForouhar, F. / Hussain, M. / Seetharaman, J. / Fang, Y. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. / Liu, J. ...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)
CitationJournal: To be Published
Title: Crystal structure of the homospermidine synthase hss from Legionella pneumophila in complex with NAD.
Authors: 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.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1873
Polymers54,4271
Non-polymers7592
Water3,225179
1
A: Homospermidine synthase
hetero molecules

A: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,3746
Polymers108,8552
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area5810 Å2
ΔGint-59 kcal/mol
Surface area36130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.848, 146.902, 85.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Homospermidine synthase


Mass: 54427.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Species: Legionella pneumophila / Strain: Philadelphia 1, DSM 7513 / Gene: hss, lpg2495 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5ZSM2, homospermidine synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 7.5, 22% PEG MME 550, 50 mM Magnesium chloride, 5 mM NAD(+), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 22, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→43.61 Å / Num. all: 40444 / Num. obs: 40444 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.069 / Net I/σ(I): 26.42
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.59 / Rsym value: 0.32 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→43.61 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 44696.79 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: XtalView program has also been used in refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3666 9.9 %RANDOM
Rwork0.202 ---
obs0.202 37042 91.6 %-
all-40444 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.3374 Å2 / ksol: 0.327013 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20 Å2
2--3.45 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 49 179 3856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.27 288 10.2 %
Rwork0.205 2539 -
obs--69.9 %

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