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- PDB-7d9i: SpdH Spermidine dehydrogenase D282A mutant -

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Basic information

Entry
Database: PDB / ID: 7d9i
TitleSpdH Spermidine dehydrogenase D282A mutant
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: 2.1 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)140,6206
Polymers137,8162
Non-polymers2,8044
Water16,015889
1
A: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3103
Polymers68,9081
Non-polymers1,4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-29 kcal/mol
Surface area21240 Å2
MethodPISA
2
B: Spermidine dehydrogenase, SpdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3103
Polymers68,9081
Non-polymers1,4022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-29 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.273, 85.762, 100.040
Angle α, β, γ (deg.)90.000, 98.353, 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: 68907.828 Da / Num. of mol.: 2 / Mutation: D282A
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.: 889 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
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: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 67104 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.68 Å2 / Rpim(I) all: 0.085 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3334 / Rpim(I) all: 0.404 / % possible all: 100

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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: 2.1→39.35 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 3227 5.04 %
Rwork0.1562 60821 -
obs0.1591 64048 94.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.64 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 0 192 891 10265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00789631
X-RAY DIFFRACTIONf_angle_d0.931813104
X-RAY DIFFRACTIONf_chiral_restr0.0521351
X-RAY DIFFRACTIONf_plane_restr0.00591705
X-RAY DIFFRACTIONf_dihedral_angle_d14.17371339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.2536810.19111494X-RAY DIFFRACTION54.18
2.13-2.160.26711290.18672261X-RAY DIFFRACTION80.61
2.16-2.20.28671210.17232362X-RAY DIFFRACTION85.39
2.2-2.240.22561240.18372510X-RAY DIFFRACTION89.59
2.24-2.280.25251490.18462511X-RAY DIFFRACTION91.63
2.28-2.320.27121500.18272613X-RAY DIFFRACTION93.19
2.32-2.370.26361550.17092602X-RAY DIFFRACTION94.51
2.37-2.420.24921440.17122618X-RAY DIFFRACTION94.75
2.42-2.480.22831360.16442695X-RAY DIFFRACTION95.48
2.48-2.540.23881240.16322721X-RAY DIFFRACTION96.47
2.54-2.610.23341350.16742738X-RAY DIFFRACTION98.12
2.61-2.680.25131280.17312826X-RAY DIFFRACTION99.46
2.68-2.770.23271500.17642774X-RAY DIFFRACTION99.8
2.77-2.870.24881390.17552787X-RAY DIFFRACTION99.97
2.87-2.980.261590.16852784X-RAY DIFFRACTION99.9
2.98-3.120.22061770.16262766X-RAY DIFFRACTION99.9
3.12-3.280.2151440.1572796X-RAY DIFFRACTION100
3.28-3.490.20041470.15282799X-RAY DIFFRACTION99.83
3.49-3.760.20141490.14442808X-RAY DIFFRACTION99.76
3.76-4.140.17131470.13192804X-RAY DIFFRACTION99.86
4.14-4.730.17331480.12442820X-RAY DIFFRACTION99.56
4.73-5.960.18011390.14122841X-RAY DIFFRACTION99.97
5.96-39.350.17811520.15562891X-RAY DIFFRACTION99.87

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