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- PDB-5equ: Crystal structure of the epimerase SnoN in complex with Fe3+, alp... -

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Basic information

Entry
Database: PDB / ID: 5equ
TitleCrystal structure of the epimerase SnoN in complex with Fe3+, alpha ketoglutarate and nogalamycin RO
ComponentsSnoN,SnoN
KeywordsISOMERASE / none-heme iron / substrate complex / nogalamycin biosynthesis
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / oxidoreductase activity / iron ion binding / metal ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nogalamycin RO / 2-OXOGLUTARIC ACID / : / SnoN / SnoN
Similarity search - Component
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSelvaraj, B. / Lindqvist, Y. / Siitonen, V. / Metsa-Ketela, M. / Schneider, G.
Funding support Sweden, Finland, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Finnish Academy Finland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Divergent non-heme iron enzymes in the nogalamycin biosynthetic pathway.
Authors: Siitonen, V. / Selvaraj, B. / Niiranen, L. / Lindqvist, Y. / Schneider, G. / Metsa-Ketela, M.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: SnoN,SnoN
B: SnoN,SnoN
C: SnoN,SnoN
D: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,92316
Polymers132,3164
Non-polymers3,60712
Water5,278293
1
A: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9814
Polymers33,0791
Non-polymers9023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9814
Polymers33,0791
Non-polymers9023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9814
Polymers33,0791
Non-polymers9023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9814
Polymers33,0791
Non-polymers9023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.908, 119.742, 159.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SnoN,SnoN


Mass: 33079.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: snoN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RN67, UniProt: Q9EYI0
#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: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-5R6 / Nogalamycin RO


Mass: 699.698 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H41NO14
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG3350, ammonium acetate, BIS-Tris, FeCl3, alpha-ketoglutarate, nogalamycin RO
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→96 Å / Num. all: 69960 / Num. obs: 69960 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.3 / Num. measured all: 282204
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.4 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EP9

5ep9


Resolution: 2.2→95.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 17.954 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23804 3423 4.9 %RANDOM
Rwork0.19929 ---
obs0.20122 66472 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.92 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→95.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7784 0 244 293 8321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198294
X-RAY DIFFRACTIONr_bond_other_d0.0090.027652
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.99911362
X-RAY DIFFRACTIONr_angle_other_deg1.6963.00917578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18951024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08321.771350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.277151150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5321586
X-RAY DIFFRACTIONr_chiral_restr0.0980.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219288
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021846
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_it0.9992.7324096
X-RAY DIFFRACTIONr_mcbond_other0.9982.7324095
X-RAY DIFFRACTIONr_mcangle_it1.6514.0945114
X-RAY DIFFRACTIONr_mcangle_other1.6514.0945115
X-RAY DIFFRACTIONr_scbond_it1.2152.8954198
X-RAY DIFFRACTIONr_scbond_other1.2152.8954199
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8024.36247
X-RAY DIFFRACTIONr_long_range_B_refined5.70224.1249557
X-RAY DIFFRACTIONr_long_range_B_other5.66423.9959499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 250 -
Rwork0.362 4791 -
obs--97.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4734-0.7806-0.13711.7432-0.39773.9082-0.0795-0.12760.20930.2354-0.04560.0066-0.10310.16620.1250.033-0.020.00230.3749-0.03360.0295-18.25619.316-1.767
23.3673-0.03310.21540.97051.09095.491-0.14280.41040.1508-0.20360.0957-0.1227-0.43640.80050.04720.0589-0.08370.01110.70910.03440.029-6.99416.815-38.227
32.40240.621-0.6911.6948-0.22955.24410.0758-0.26330.11630.2672-0.1783-0.1597-0.49420.5480.10250.0868-0.0381-0.03740.63250.03860.03362.76-1.13437.321
41.2363-0.36450.83243.0624-0.56834.75680.08130.2046-0.2353-0.5413-0.2004-0.16640.94570.13410.1190.27840.11590.07760.6533-0.02150.0789-1.712-12.3271.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 272
2X-RAY DIFFRACTION2B17 - 272
3X-RAY DIFFRACTION3C17 - 272
4X-RAY DIFFRACTION4D17 - 272

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