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- PDB-7d9j: SpdH Spermidine dehydrogenase Y443A mutant -

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Basic information

Entry
Database: PDB / ID: 7d9j
TitleSpdH Spermidine dehydrogenase Y443A mutant
ComponentsSpermidine dehydrogenase, SpdH
KeywordsOXIDOREDUCTASE / SpdH / Spermidine dehydrogenase / Heme-containing monoamine oxidase / Pseudomonas aeruginosa PAO1.
Function / homologyNAD(P)-binding Rossmann-like domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Spermidine dehydrogenase, SpdH
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsChe, S. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: Febs J. / Year: 2022
Title: Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.
Authors: Che, S. / Liang, Y. / Chen, Y. / Wu, W. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionOct 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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: Spermidine dehydrogenase, SpdH
B: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,6167
Polymers137,7192
Non-polymers2,8965
Water19,4201078
1
A: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3544
Polymers68,8601
Non-polymers1,4943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-29 kcal/mol
Surface area20950 Å2
MethodPISA
2
B: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2623
Polymers68,8601
Non-polymers1,4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-30 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.051, 85.501, 101.109
Angle α, β, γ (deg.)90.000, 98.463, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Spermidine dehydrogenase, SpdH /


Mass: 68859.742 Da / Num. of mol.: 2 / Mutation: Y443A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: spdH, PA3713 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HXS8, EC: 1.5.99.6
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1078 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis Tris pH6.5, 20% w/v polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97737 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97737 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 59220 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.5 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 18.2
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5 / Num. unique obs: 2898 / Rpim(I) all: 0.144 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D9F

7d9f


Resolution: 2.19→34.96 Å / SU ML: 0.2112 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2837
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203 2919 4.93 %
Rwork0.1466 56232 -
obs0.1494 59151 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.73 Å2
Refinement stepCycle: LAST / Resolution: 2.19→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9159 0 198 1078 10435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00779610
X-RAY DIFFRACTIONf_angle_d0.905913073
X-RAY DIFFRACTIONf_chiral_restr0.05211349
X-RAY DIFFRACTIONf_plane_restr0.00611702
X-RAY DIFFRACTIONf_dihedral_angle_d18.67943482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.230.32171370.1832435X-RAY DIFFRACTION91.11
2.23-2.270.25131420.16672646X-RAY DIFFRACTION98.83
2.27-2.310.22441540.1582646X-RAY DIFFRACTION98.84
2.31-2.350.2481350.15942649X-RAY DIFFRACTION98.9
2.35-2.40.24661350.15942697X-RAY DIFFRACTION98.95
2.4-2.450.21941430.16112654X-RAY DIFFRACTION99.01
2.45-2.510.26211290.15672696X-RAY DIFFRACTION99.19
2.51-2.570.22111250.15752659X-RAY DIFFRACTION99.15
2.57-2.640.23851420.15092696X-RAY DIFFRACTION99.16
2.64-2.720.22261280.15632665X-RAY DIFFRACTION99.29
2.72-2.810.22531390.15572699X-RAY DIFFRACTION99.27
2.81-2.910.24421270.15892713X-RAY DIFFRACTION99.51
2.91-3.020.19561290.16132697X-RAY DIFFRACTION99.54
3.02-3.160.23081440.16322713X-RAY DIFFRACTION99.44
3.16-3.330.23581260.15952693X-RAY DIFFRACTION99.65
3.33-3.540.21161400.15512691X-RAY DIFFRACTION99.26
3.54-3.810.18881550.14042680X-RAY DIFFRACTION99.61
3.81-4.190.18111630.12522694X-RAY DIFFRACTION99.72
4.19-4.80.14071520.11212700X-RAY DIFFRACTION99.86
4.8-6.040.16231510.13082724X-RAY DIFFRACTION99.62
6.04-34.960.17651230.14462785X-RAY DIFFRACTION98.61

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