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- PDB-5zm2: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA -

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Basic information

Entry
Database: PDB / ID: 5zm2
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA
ComponentsDioxygenase andA
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / terpenoid biosynthetic process / dioxygenase activity / metal ion binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEmericella variicolor (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNakashima, Y. / Senda, T.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis.
Authors: Nakashima, Y. / Mitsuhashi, T. / Matsuda, Y. / Senda, M. / Sato, H. / Yamazaki, M. / Uchiyama, M. / Senda, T. / Abe, I.
History
DepositionApr 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dioxygenase andA
B: Dioxygenase andA
C: Dioxygenase andA
D: Dioxygenase andA


Theoretical massNumber of molelcules
Total (without water)135,4184
Polymers135,4184
Non-polymers00
Water4,414245
1
A: Dioxygenase andA
B: Dioxygenase andA


Theoretical massNumber of molelcules
Total (without water)67,7092
Polymers67,7092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-19 kcal/mol
Surface area20370 Å2
MethodPISA
2
C: Dioxygenase andA

D: Dioxygenase andA


Theoretical massNumber of molelcules
Total (without water)67,7092
Polymers67,7092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area3050 Å2
ΔGint-24 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.954, 74.887, 87.450
Angle α, β, γ (deg.)103.95, 108.22, 90.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dioxygenase andA / Anditomin synthesis protein A


Mass: 33854.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella variicolor (mold) / Gene: andA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A097ZPD5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% (w/v) PEG 3350, 200mM sodium tartrate, 20% DMF

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.55 Å / Num. obs: 48298 / % possible obs: 96.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.55 Å / Rmerge(I) obs: 0.511 / Num. unique obs: 4442

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBM

5ybm


Resolution: 2.5→47.078 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.55
RfactorNum. reflection% reflection
Rfree0.253 2530 5.24 %
Rwork0.1976 --
obs0.2004 48297 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 0 245 8337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088265
X-RAY DIFFRACTIONf_angle_d1.00211271
X-RAY DIFFRACTIONf_dihedral_angle_d15.2414981
X-RAY DIFFRACTIONf_chiral_restr0.0531278
X-RAY DIFFRACTIONf_plane_restr0.0071507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55090.3091390.27042649X-RAY DIFFRACTION92
2.5509-2.60630.35821390.27422651X-RAY DIFFRACTION91
2.6063-2.66670.27781260.26772691X-RAY DIFFRACTION92
2.6667-2.73320.33211260.25072698X-RAY DIFFRACTION91
2.7332-2.80690.35711190.24112652X-RAY DIFFRACTION90
2.8069-2.88920.31011540.23252596X-RAY DIFFRACTION89
2.8892-2.98210.27321390.21682642X-RAY DIFFRACTION89
2.9821-3.08830.26811460.21892649X-RAY DIFFRACTION91
3.0883-3.21140.28731440.20542710X-RAY DIFFRACTION92
3.2114-3.35680.24981660.1942697X-RAY DIFFRACTION92
3.3568-3.53270.24621360.17692730X-RAY DIFFRACTION94
3.5327-3.75240.21861180.17622805X-RAY DIFFRACTION95
3.7524-4.03960.22231480.1662722X-RAY DIFFRACTION94
4.0396-4.44140.19381510.15232738X-RAY DIFFRACTION93
4.4414-5.07320.18651500.15332727X-RAY DIFFRACTION93
5.0732-6.35160.2721500.20952732X-RAY DIFFRACTION93
6.3516-18.96820.25281520.20142710X-RAY DIFFRACTION92

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