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- PDB-6y87: Crystal Structure of the Homospermidine Synthase (HSS) from Pseud... -

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Basic information

Entry
Database: PDB / ID: 6y87
TitleCrystal Structure of the Homospermidine Synthase (HSS) from Pseudomonas aeruginosa in Complex with NAD and PUT
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / Homospermidine Synthase / Rossmann Fold / NAD / Putrescine
Function / homology
Function and homology information


homospermidine synthase / homospermidine synthase activity / nucleotide binding
Similarity search - Function
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIAMINOBUTANE / Homospermidine synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHelfrich, F. / Scheidig, A.J.
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-pi interaction.
Authors: Helfrich, F. / Scheidig, A.J.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionMar 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homospermidine synthase
B: Homospermidine synthase
C: Homospermidine synthase
D: Homospermidine synthase
E: Homospermidine synthase
F: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,29215
Polymers312,0476
Non-polymers4,2459
Water22,3751242
1
A: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7593
Polymers52,0081
Non-polymers7522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6712
Polymers52,0081
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7593
Polymers52,0081
Non-polymers7522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6712
Polymers52,0081
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7593
Polymers52,0081
Non-polymers7522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6712
Polymers52,0081
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.242, 103.242, 548.005
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Space group name HallP322(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11F-717-

HOH

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Components

#1: Protein
Homospermidine synthase / Putative homospermidine synthase


Mass: 52007.777 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: CL-17, hss, DY940_20665, DZ962_18725, IPC1481_09030, IPC1509_31480, IPC669_32825, PACL_0336, PACL_0523, PAMH19_5634
Production host: Escherichia coli (E. coli) / References: UniProt: Q6X2Y9, homospermidine synthase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: HEPES, Poly(acrylic acid sodium salt) 5,100, agmatine sulfate, ATP

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→85 Å / Num. obs: 179714 / % possible obs: 98.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 28.46 Å2 / CC1/2: 0.974 / CC star: 0.993 / Net I/σ(I): 5.1
Reflection shellResolution: 2.15→2.19 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 8374 / Rpim(I) all: 1.325 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALAdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLP

4plp


Resolution: 2.15→80.31 Å / SU ML: 0.3002 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.6878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 8591 4.8 %
Rwork0.2029 170419 -
obs0.2049 179010 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 2.15→80.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21569 0 282 1242 23093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002922472
X-RAY DIFFRACTIONf_angle_d0.670530650
X-RAY DIFFRACTIONf_chiral_restr0.04233448
X-RAY DIFFRACTIONf_plane_restr0.00273861
X-RAY DIFFRACTIONf_dihedral_angle_d17.81588123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.35072220.30644839X-RAY DIFFRACTION85.49
2.17-2.20.32882930.29955494X-RAY DIFFRACTION95.17
2.2-2.230.34772450.29035604X-RAY DIFFRACTION97.84
2.23-2.260.33113200.28775602X-RAY DIFFRACTION97.82
2.26-2.280.30922660.27045644X-RAY DIFFRACTION97.9
2.28-2.320.31222580.27315631X-RAY DIFFRACTION98.07
2.32-2.350.32643090.27095673X-RAY DIFFRACTION98.13
2.35-2.380.2883150.26655572X-RAY DIFFRACTION98.05
2.38-2.420.31522970.25695604X-RAY DIFFRACTION98.2
2.42-2.460.28312640.25225759X-RAY DIFFRACTION98.24
2.46-2.50.27743000.24825563X-RAY DIFFRACTION98.27
2.5-2.550.28822830.24625661X-RAY DIFFRACTION98.41
2.55-2.60.3023100.25475671X-RAY DIFFRACTION98.58
2.6-2.650.2922870.24165686X-RAY DIFFRACTION98.16
2.65-2.710.30262660.2355700X-RAY DIFFRACTION98.53
2.71-2.770.26642960.22165618X-RAY DIFFRACTION98.63
2.77-2.840.27052950.21565710X-RAY DIFFRACTION98.83
2.84-2.920.25132760.20625729X-RAY DIFFRACTION98.85
2.92-30.24973040.20315690X-RAY DIFFRACTION98.94
3-3.10.23683050.20515714X-RAY DIFFRACTION99.05
3.1-3.210.23432720.20195754X-RAY DIFFRACTION99.06
3.21-3.340.2342980.19045728X-RAY DIFFRACTION99.11
3.34-3.490.2292230.18275809X-RAY DIFFRACTION99.31
3.49-3.680.22412660.17965826X-RAY DIFFRACTION99.3
3.68-3.910.20712950.16915736X-RAY DIFFRACTION99.24
3.91-4.210.2132980.15755788X-RAY DIFFRACTION99.49
4.21-4.630.17542950.14665833X-RAY DIFFRACTION99.58
4.63-5.30.19223100.1455828X-RAY DIFFRACTION99.68
5.3-6.680.21473020.18035897X-RAY DIFFRACTION99.73
6.68-80.310.21483210.18726056X-RAY DIFFRACTION99.59

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