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- PDB-8w8h: 2-Ketoglutarate-Dependent Dioxygenase -

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Basic information

Entry
Database: PDB / ID: 8w8h
Title2-Ketoglutarate-Dependent Dioxygenase
Components2OG-Fe dioxygenase family protein
KeywordsOXIDOREDUCTASE / Tetramer / Metalloenzyme / Hydroxylation activity
Function / homologyISOLEUCINE / :
Function and homology information
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZheng, C.N. / Wei, W.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: a Fe(2)/2-KG dioxygenases from Bacillus licheniformis
Authors: Zheng, C.N. / Wei, W.Q.
History
DepositionSep 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2OG-Fe dioxygenase family protein
B: 2OG-Fe dioxygenase family protein
C: 2OG-Fe dioxygenase family protein
D: 2OG-Fe dioxygenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,73812
Polymers118,6884
Non-polymers1,0498
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-2 kcal/mol
Surface area38940 Å2
Unit cell
Length a, b, c (Å)45.145, 129.628, 153.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
2OG-Fe dioxygenase family protein


Mass: 29672.068 Da / Num. of mol.: 4 / Mutation: S18A, Q164K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: CJ481_05930 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A5I123
#2: Chemical
ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
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: 1.89 Å3/Da / Density % sol: 35.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 17 mg/mL enzyme was incubated with 9.2 mM L-Ile and grew at 1 M sodium citrate for 15 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→23.65 Å / Num. obs: 15586 / % possible obs: 99.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.227 / Net I/σ(I): 7.2
Reflection shellResolution: 3.2→3.46 Å / Rmerge(I) obs: 0.606 / Num. unique obs: 3153

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→23.65 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.877 / SU B: 32.162 / SU ML: 0.518 / Cross valid method: THROUGHOUT / ESU R Free: 0.626 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26674 826 5.3 %RANDOM
Rwork0.21585 ---
obs0.21863 14714 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.796 Å2
Baniso -1Baniso -2Baniso -3
1-7.66 Å2-0 Å20 Å2
2---2.55 Å2-0 Å2
3----5.11 Å2
Refinement stepCycle: 1 / Resolution: 3.2→23.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7536 0 72 0 7608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197786
X-RAY DIFFRACTIONr_bond_other_d0.0010.027175
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9510565
X-RAY DIFFRACTIONr_angle_other_deg0.702316527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31424.444405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.042151280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1211546
X-RAY DIFFRACTIONr_chiral_restr0.0690.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2345.3723776
X-RAY DIFFRACTIONr_mcbond_other2.2345.3723775
X-RAY DIFFRACTIONr_mcangle_it3.8938.0584699
X-RAY DIFFRACTIONr_mcangle_other3.8928.0584700
X-RAY DIFFRACTIONr_scbond_it1.8675.5034010
X-RAY DIFFRACTIONr_scbond_other1.8665.5044010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3248.185867
X-RAY DIFFRACTIONr_long_range_B_refined6.20461.9128314
X-RAY DIFFRACTIONr_long_range_B_other6.20461.9138315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A74980.07
12B74980.07
21A73990.08
22C73990.08
31A74950.07
32D74950.07
41B75060.07
42C75060.07
51B75440.07
52D75440.07
61C74630.08
62D74630.08
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 56 -
Rwork0.312 1068 -
obs--100 %

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