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- PDB-5zm3: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with prean... -

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Basic information

Entry
Database: PDB / ID: 5zm3
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B
ComponentsDioxygenase andA
KeywordsOXIDOREDUCTASE / Oxygenase
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
Chem-9FR / 2-OXOGLUTARIC ACID / : / Dioxygenase andA
Similarity search - Component
Biological speciesEmericella variicolor (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,87516
Polymers135,4184
Non-polymers2,45812
Water7,620423
1
A: Dioxygenase andA
hetero molecules

D: Dioxygenase andA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9388
Polymers67,7092
Non-polymers1,2296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area5450 Å2
ΔGint-56 kcal/mol
Surface area20300 Å2
MethodPISA
2
B: Dioxygenase andA
hetero molecules

C: Dioxygenase andA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9388
Polymers67,7092
Non-polymers1,2296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5440 Å2
ΔGint-55 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.642, 73.340, 86.971
Angle α, β, γ (deg.)75.97, 71.35, 89.68
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: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H6O5
#4: Chemical
ChemComp-9FR / (6aS,8aR,12aS,12bR,13aR)-5,6a,9,9,12a,13a-hexamethyl-7,8,8a,9,11,12,12a,12b,13,13a-decahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1H,6aH)-trione / Preandiloid B


Mass: 412.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H32O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
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: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→47.35 Å / Num. obs: 65777 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4
Reflection shellResolution: 2.25→2.3 Å / Rmerge(I) obs: 0.513 / Num. unique obs: 4400

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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: 2.25→47.293 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.84
RfactorNum. reflection% reflection
Rfree0.2737 3428 5.21 %
Rwork0.213 --
obs0.2163 65772 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→47.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8668 0 164 423 9255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089032
X-RAY DIFFRACTIONf_angle_d0.99312343
X-RAY DIFFRACTIONf_dihedral_angle_d17.5575417
X-RAY DIFFRACTIONf_chiral_restr0.0561379
X-RAY DIFFRACTIONf_plane_restr0.0071633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2502-2.2890.31331870.26273079X-RAY DIFFRACTION91
2.289-2.33050.29591540.26443070X-RAY DIFFRACTION92
2.3305-2.37530.32931660.25433094X-RAY DIFFRACTION92
2.3753-2.42380.36461350.26673170X-RAY DIFFRACTION93
2.4238-2.47640.29491800.25553061X-RAY DIFFRACTION92
2.4764-2.5340.32321590.24663123X-RAY DIFFRACTION93
2.534-2.59730.3461720.24743088X-RAY DIFFRACTION92
2.5973-2.66740.33161510.25523104X-RAY DIFFRACTION93
2.6674-2.74580.34291630.23963129X-RAY DIFFRACTION92
2.7458-2.83430.29461630.23383132X-RAY DIFFRACTION93
2.8343-2.93550.29331690.22383073X-RAY DIFFRACTION92
2.9355-3.05280.2761520.22143141X-RAY DIFFRACTION93
3.0528-3.19150.28671410.21323190X-RAY DIFFRACTION94
3.1915-3.35940.27091490.19873096X-RAY DIFFRACTION93
3.3594-3.56930.27691680.19033154X-RAY DIFFRACTION94
3.5693-3.8440.23291800.18423152X-RAY DIFFRACTION93
3.844-4.22910.25051690.17863159X-RAY DIFFRACTION94
4.2291-4.83720.22061500.16383173X-RAY DIFFRACTION94
4.8372-6.07960.25521820.21013136X-RAY DIFFRACTION94
6.0796-24.90290.24241780.22153133X-RAY DIFFRACTION93

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