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- PDB-9c9n: Crystal structure of Fe/2-OG dependent dioxygenase MysH in comple... -

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Basic information

Entry
Database: PDB / ID: 9c9n
TitleCrystal structure of Fe/2-OG dependent dioxygenase MysH in complex with nickel and succinate
ComponentsFe/2-OG dependent dioxygenase MysH
KeywordsMETAL BINDING PROTEIN / Non-heme iron dependent / dioxygenase / jelly roll fold / phytanoyl-CoA dioxygenase family protein
Function / homologyACETATE ION / NICKEL (II) ION / SUCCINIC ACID
Function and homology information
Biological speciesNostoc linckia NIES-25 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWanniarachchi, T.N. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2108383 United States
CitationJournal: To Be Published
Title: Crystal structure of non-heme iron and alpha-ketoglutarate dependent dioxygenase MysH (To be published)
Authors: Wanniarachchi, T.N. / Bruner, S.D.
History
DepositionJun 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe/2-OG dependent dioxygenase MysH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3495
Polymers31,0511
Non-polymers2984
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.291, 44.291, 107.349
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fe/2-OG dependent dioxygenase MysH


Mass: 31051.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein was expressed with a hexa-Histidine tag that was cleaved using TEV protease before crystallization
Source: (gene. exp.) Nostoc linckia NIES-25 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 222 molecules

#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.3 M Sodium acetate trihydrate, 0.1 M TRIS hydrochloride pH 8.5, 35 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.45→26.17 Å / Num. obs: 41408 / % possible obs: 99.88 % / Redundancy: 5.9 % / Biso Wilson estimate: 14.07 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.0917 / Rpim(I) all: 0.04069 / Rrim(I) all: 0.1004 / Net I/σ(I): 10.45
Reflection shellResolution: 1.454→1.506 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.6488 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 4122 / CC1/2: 0.785 / CC star: 0.938 / Rpim(I) all: 0.3016 / Rrim(I) all: 0.7169 / % possible all: 99.11

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→26.17 Å / SU ML: 0.1347 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.8295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2064 2067 4.99 %
Rwork0.1841 39338 -
obs0.1851 41405 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.74 Å2
Refinement stepCycle: LAST / Resolution: 1.45→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 17 218 2363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532202
X-RAY DIFFRACTIONf_angle_d0.8512987
X-RAY DIFFRACTIONf_chiral_restr0.083315
X-RAY DIFFRACTIONf_plane_restr0.007386
X-RAY DIFFRACTIONf_dihedral_angle_d14.511815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.27271560.2512561X-RAY DIFFRACTION98.66
1.49-1.520.26861520.22712651X-RAY DIFFRACTION100
1.52-1.570.25231180.20872634X-RAY DIFFRACTION100
1.57-1.610.2662020.21022535X-RAY DIFFRACTION99.96
1.61-1.660.2165940.21692668X-RAY DIFFRACTION99.96
1.66-1.720.23171110.2142640X-RAY DIFFRACTION100
1.72-1.790.22191520.20022612X-RAY DIFFRACTION100
1.79-1.870.23231200.20482650X-RAY DIFFRACTION100
1.87-1.970.21641820.21152582X-RAY DIFFRACTION100
1.97-2.10.23271520.20212623X-RAY DIFFRACTION100
2.1-2.260.22291120.19292636X-RAY DIFFRACTION100
2.26-2.490.22861230.18752667X-RAY DIFFRACTION100
2.49-2.840.2191370.19262608X-RAY DIFFRACTION100
2.84-3.580.18221220.17292627X-RAY DIFFRACTION100
3.58-26.170.14391340.13582644X-RAY DIFFRACTION99.96

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