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- PDB-9pze: Crystal structure of Fe/2-OG dependent dioxygenase MysH with dock... -

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Basic information

Entry
Database: PDB / ID: 9pze
TitleCrystal structure of Fe/2-OG dependent dioxygenase MysH with docked C-terminus
ComponentsFe/2-OG dependent dioxygenase MysH
KeywordsMETAL BINDING PROTEIN / Non-heme iron dependent / dioxygenase / jelly roll fold / phytanoyl-CoA / dioxygenase family protein
Function / homology: / CITRATE ANION
Function and homology information
Biological speciesNostoc linckia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: 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
B: Fe/2-OG dependent dioxygenase MysH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0546
Polymers63,5642
Non-polymers4904
Water7,332407
1
A: Fe/2-OG dependent dioxygenase MysH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0273
Polymers31,7821
Non-polymers2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fe/2-OG dependent dioxygenase MysH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0273
Polymers31,7821
Non-polymers2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.505, 142.701, 44.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 31781.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NCBI Reference Sequence: WP_096541772.1 / Source: (gene. exp.) Nostoc linckia (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 5.5 / Details: 20% PEG 3000, citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.679→41.9 Å / Num. obs: 124593 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.84
Reflection shellResolution: 1.68→1.7 Å / Mean I/σ(I) obs: 2.18 / Num. unique obs: 54 / CC1/2: 0.737

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→41.9 Å / SU ML: 0.213 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2152 3277 5.01 %
Rwork0.1808 62164 -
obs0.1825 65441 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.29 Å2
Refinement stepCycle: LAST / Resolution: 1.68→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 28 407 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624266
X-RAY DIFFRACTIONf_angle_d0.86725802
X-RAY DIFFRACTIONf_chiral_restr0.0575604
X-RAY DIFFRACTIONf_plane_restr0.0096748
X-RAY DIFFRACTIONf_dihedral_angle_d14.09521558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.30711370.29122618X-RAY DIFFRACTION97.97
1.7-1.730.26091440.25442643X-RAY DIFFRACTION100
1.73-1.760.26911300.23642658X-RAY DIFFRACTION100
1.76-1.790.28531420.22432693X-RAY DIFFRACTION100
1.79-1.820.25061290.21882662X-RAY DIFFRACTION100
1.82-1.860.29191540.21692665X-RAY DIFFRACTION100
1.86-1.890.21981530.19882649X-RAY DIFFRACTION100
1.89-1.940.22051550.19642698X-RAY DIFFRACTION100
1.94-1.980.25491500.19712652X-RAY DIFFRACTION100
1.98-2.030.21891320.18552699X-RAY DIFFRACTION100
2.03-2.090.22991490.18562647X-RAY DIFFRACTION100
2.09-2.150.22341590.19162687X-RAY DIFFRACTION100
2.15-2.220.23831330.19412695X-RAY DIFFRACTION100
2.22-2.30.22521340.18692674X-RAY DIFFRACTION100
2.3-2.390.19431350.18222720X-RAY DIFFRACTION100
2.39-2.50.25271510.18152711X-RAY DIFFRACTION99.97
2.5-2.630.22391440.19662714X-RAY DIFFRACTION100
2.63-2.790.24181440.19482706X-RAY DIFFRACTION99.96
2.79-3.010.23431390.19352725X-RAY DIFFRACTION100
3.01-3.310.21471560.17832720X-RAY DIFFRACTION100
3.31-3.790.20561220.15282778X-RAY DIFFRACTION99.97
3.79-4.770.151360.14332799X-RAY DIFFRACTION100
4.77-41.90.19291490.17442951X-RAY DIFFRACTION99.94

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