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- PDB-7d9h: SpdH Spermidine dehydrogenase N33 truncation structure -

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Basic information

Entry
Database: PDB / ID: 7d9h
TitleSpdH Spermidine dehydrogenase N33 truncation 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 / MOLECULAR REPLACEMENT / Resolution: 2.31 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)134,1008
Polymers131,1122
Non-polymers2,9886
Water13,962775
1
A: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0504
Polymers65,5561
Non-polymers1,4943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-30 kcal/mol
Surface area21270 Å2
MethodPISA
2
B: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0504
Polymers65,5561
Non-polymers1,4943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-29 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.284, 84.926, 101.081
Angle α, β, γ (deg.)90.000, 98.396, 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: 65555.867 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
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
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: BL19U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 48990 / % possible obs: 96.8 % / Redundancy: 3 % / Biso Wilson estimate: 28.43 Å2 / Rpim(I) all: 0.037 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Mean I/σ(I) obs: 7.7 / Num. unique obs: 2445 / Rpim(I) all: 0.089 / % possible all: 97.8

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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: 2.31→38.74 Å / SU ML: 0.2546 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2143 2518 5.15 %
Rwork0.1509 46406 -
obs0.1542 48924 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.47 Å2
Refinement stepCycle: LAST / Resolution: 2.31→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 204 775 10115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819592
X-RAY DIFFRACTIONf_angle_d0.942513044
X-RAY DIFFRACTIONf_chiral_restr0.05171343
X-RAY DIFFRACTIONf_plane_restr0.00611695
X-RAY DIFFRACTIONf_dihedral_angle_d19.27943474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.26431320.15942328X-RAY DIFFRACTION87.76
2.36-2.40.26191220.16632601X-RAY DIFFRACTION96.15
2.4-2.460.24251230.15762520X-RAY DIFFRACTION95.73
2.46-2.510.27011510.15462557X-RAY DIFFRACTION96.4
2.51-2.580.23791370.15942519X-RAY DIFFRACTION93.49
2.58-2.650.24191250.16822546X-RAY DIFFRACTION95.15
2.65-2.720.25151520.16822540X-RAY DIFFRACTION96.07
2.72-2.810.23711490.17912564X-RAY DIFFRACTION95.97
2.81-2.910.27341480.17252580X-RAY DIFFRACTION97.05
2.91-3.030.25821340.1692585X-RAY DIFFRACTION97
3.03-3.170.27821440.17852601X-RAY DIFFRACTION96.69
3.17-3.330.23841490.17042603X-RAY DIFFRACTION97.94
3.33-3.540.2291510.16032648X-RAY DIFFRACTION98.38
3.54-3.820.19291340.15382621X-RAY DIFFRACTION98.08
3.82-4.20.16871340.12862634X-RAY DIFFRACTION97.5
4.2-4.810.1641530.11722633X-RAY DIFFRACTION98.31
4.81-6.050.17821510.12642668X-RAY DIFFRACTION98.57
6.05-38.740.15821290.13792658X-RAY DIFFRACTION95.61

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