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- PDB-7d9f: SpdH Spermidine dehydrogenase SeMet Structure -

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Basic information

Entry
Database: PDB / ID: 7d9f
TitleSpdH Spermidine dehydrogenase SeMet Structure
ComponentsSpermidine dehydrogenase, SpdH
KeywordsOXIDOREDUCTASE / SpdH / Spermidine dehydrogenase / Heme-containing monoamine oxidase / Pseudomonas aeruginosa PAO1.
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
NAD(P)-binding Rossmann-like domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Spermidine dehydrogenase, SpdH
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)142,76512
Polymers139,4042
Non-polymers3,36110
Water21,7621208
1
A: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3846
Polymers69,7021
Non-polymers1,6825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-44 kcal/mol
Surface area21800 Å2
MethodPISA
2
B: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3806
Polymers69,7021
Non-polymers1,6785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-30 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.197, 85.586, 99.624
Angle α, β, γ (deg.)90.000, 98.326, 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

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Protein , 1 types, 2 molecules AB

#1: Protein Spermidine dehydrogenase, SpdH


Mass: 69702.172 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 1218 molecules

#2: Chemical ChemComp-FAD / 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


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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: 0.97778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 95318 / % possible obs: 97.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.27 Å2 / Rpim(I) all: 0.057 / Net I/σ(I): 13.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4659 / Rpim(I) all: 0.345 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→39.25 Å / SU ML: 0.1688 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 3498 2.17 %
Rwork0.1503 157646 -
obs0.1511 92457 83.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.73 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9278 0 227 1208 10713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00659758
X-RAY DIFFRACTIONf_angle_d0.83613268
X-RAY DIFFRACTIONf_chiral_restr0.05241362
X-RAY DIFFRACTIONf_plane_restr0.00571727
X-RAY DIFFRACTIONf_dihedral_angle_d18.17043543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.2266690.20193123X-RAY DIFFRACTION41.38
1.88-1.910.2258790.19883592X-RAY DIFFRACTION47.85
1.91-1.930.2345900.18984067X-RAY DIFFRACTION53.82
1.93-1.960.2683960.18694363X-RAY DIFFRACTION58.36
1.96-20.19851040.17744647X-RAY DIFFRACTION62.19
2-2.030.21691130.17395020X-RAY DIFFRACTION66.44
2.03-2.070.20661170.17145317X-RAY DIFFRACTION71.42
2.07-2.110.1771330.16575838X-RAY DIFFRACTION77.84
2.11-2.150.20911360.16286142X-RAY DIFFRACTION81.42
2.15-2.20.22121450.1646566X-RAY DIFFRACTION87.07
2.2-2.250.16691540.16376787X-RAY DIFFRACTION90.06
2.25-2.310.22061540.16956915X-RAY DIFFRACTION92.02
2.31-2.370.20911580.16187030X-RAY DIFFRACTION94.75
2.37-2.440.22741590.16227201X-RAY DIFFRACTION95.08
2.44-2.520.20641610.16267113X-RAY DIFFRACTION95.35
2.52-2.610.19111560.15627203X-RAY DIFFRACTION96.06
2.61-2.710.23891640.16237360X-RAY DIFFRACTION97.66
2.71-2.830.22461620.15487390X-RAY DIFFRACTION98.15
2.83-2.980.19461620.15337363X-RAY DIFFRACTION98.07
2.98-3.170.18341620.15187374X-RAY DIFFRACTION98.15
3.17-3.410.19581650.14167446X-RAY DIFFRACTION99.26
3.41-3.760.18861670.13137424X-RAY DIFFRACTION98.88
3.76-4.30.16361650.12047492X-RAY DIFFRACTION99.24
4.3-5.420.13071620.12637429X-RAY DIFFRACTION99.24
5.42-39.250.17461650.1527444X-RAY DIFFRACTION99.19

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