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- PDB-7d9g: SpdH Spermidine dehydrogenase native structure -

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Basic information

Entry
Database: PDB / ID: 7d9g
TitleSpdH Spermidine dehydrogenase native structure
ComponentsSpermidine dehydrogenase, SpdH
KeywordsOXIDOREDUCTASE / SpdH / Spermidine dehydrogenase / Heme-containing monoamine oxidase / Pseudomonas aeruginosa PAO1.
Function / homology
Function and homology information


phytoene dehydrogenase activity / carotenoid biosynthetic process / 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: 2.4 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)140,7086
Polymers137,9042
Non-polymers2,8044
Water10,755597
1
A: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3543
Polymers68,9521
Non-polymers1,4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-19 kcal/mol
Surface area22040 Å2
MethodPISA
2
B: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3543
Polymers68,9521
Non-polymers1,4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-20 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.399, 85.731, 100.654
Angle α, β, γ (deg.)90.000, 98.448, 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: 68951.836 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis tris pH 6.5, 20% w/v polyethylene glycol 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: Oct 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45554 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.61 Å2 / Rpim(I) all: 0.077 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2136 / Rpim(I) all: 0.241 / % possible all: 94.6

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Processing

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

7d9f


Resolution: 2.4→49.78 Å / SU ML: 0.2944 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0415
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 3888 4.39 %
Rwork0.1832 84664 -
obs0.1859 45510 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9240 0 192 597 10029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919688
X-RAY DIFFRACTIONf_angle_d0.987613178
X-RAY DIFFRACTIONf_chiral_restr0.05231357
X-RAY DIFFRACTIONf_plane_restr0.00651717
X-RAY DIFFRACTIONf_dihedral_angle_d16.45133516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.33341170.26542546X-RAY DIFFRACTION85.79
2.43-2.460.27391350.24422847X-RAY DIFFRACTION91.25
2.46-2.490.31571310.24092890X-RAY DIFFRACTION95.21
2.49-2.530.26291380.24562979X-RAY DIFFRACTION97.28
2.53-2.560.30471370.23783041X-RAY DIFFRACTION98.21
2.56-2.60.31051390.2343047X-RAY DIFFRACTION99.13
2.6-2.640.35881410.23693042X-RAY DIFFRACTION99.44
2.64-2.680.27441420.22833066X-RAY DIFFRACTION99.78
2.68-2.730.30071400.22773028X-RAY DIFFRACTION99.75
2.73-2.780.26761440.22143095X-RAY DIFFRACTION99.75
2.78-2.830.27531390.22033031X-RAY DIFFRACTION99.87
2.83-2.890.33291450.22113090X-RAY DIFFRACTION99.94
2.89-2.950.29381420.21323080X-RAY DIFFRACTION99.88
2.95-3.020.3121370.21893032X-RAY DIFFRACTION99.91
3.02-3.10.25121390.20593026X-RAY DIFFRACTION99.87
3.1-3.180.27841420.21013082X-RAY DIFFRACTION100
3.18-3.280.23641390.19833048X-RAY DIFFRACTION100
3.28-3.380.31741410.19323073X-RAY DIFFRACTION99.88
3.38-3.50.28521420.18613075X-RAY DIFFRACTION99.94
3.5-3.640.22691390.17283082X-RAY DIFFRACTION100
3.64-3.810.2491400.16233053X-RAY DIFFRACTION100
3.81-4.010.23731390.15723048X-RAY DIFFRACTION99.97
4.01-4.260.20421410.14023099X-RAY DIFFRACTION100
4.26-4.590.14771420.1273096X-RAY DIFFRACTION99.97
4.59-5.050.18781380.13723029X-RAY DIFFRACTION99.97
5.05-5.780.18471350.14743076X-RAY DIFFRACTION99.88
5.78-7.280.23161440.16183054X-RAY DIFFRACTION99.97
7.28-49.780.18061400.14133009X-RAY DIFFRACTION98.19
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.125756027940.2310625515880.2817874391280.3783461772110.104275688410.3152991289630.0617533119531-0.0579190830842-0.03745778609090.0428257452127-0.0182407093167-0.009730142733820.0205655715151-0.0506575167738-0.04320937729910.2268662995662.75879688638E-50.006236623252570.220231103710.02385262221840.209603032366-10.193663789-7.91286127487-7.66249352759
20.8616356569620.0218506370790.2399821642050.380110958268-0.08032230670030.380450370630.01957254110030.0586708409326-0.0775181890724-0.0394366214074-0.009716383045840.00789581385450.07103552475540.0127972081071-0.0115336161930.2044294080430.001402012191640.001077770863990.2023791652655.48532826286E-50.2402354187170.0919528680036-3.84914039235-55.4638921653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 33 THROUGH 619)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 32 THROUGH 619)

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