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- PDB-5ep9: Crystal structure of the non-heme alpha ketoglutarate dependent e... -

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Basic information

Entry
Database: PDB / ID: 5ep9
TitleCrystal structure of the non-heme alpha ketoglutarate dependent epimerase SnoN from nogalamycin biosynthesis
ComponentsSnoN,Epimerase SnoN
KeywordsMETAL BINDING PROTEIN / polyketide biosynthesis / iron center
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
ACETATE ION / 2-OXOGLUTARIC ACID / : / SnoN / SnoN
Similarity search - Component
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSelvaraj, B. / Lindqvist, Y. / Niiranen, L. / 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 11, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SnoN,Epimerase SnoN
B: SnoN,Epimerase SnoN
C: SnoN,Epimerase SnoN
D: SnoN,Epimerase SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,18313
Polymers132,3164
Non-polymers8679
Water8,233457
1
A: SnoN,Epimerase SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3404
Polymers33,0791
Non-polymers2613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SnoN,Epimerase SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2813
Polymers33,0791
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SnoN,Epimerase SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2813
Polymers33,0791
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SnoN,Epimerase SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2813
Polymers33,0791
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.207, 120.557, 102.879
Angle α, β, γ (deg.)90.00, 92.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 17 - 272 / Label seq-ID: 29 - 284

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
SnoN,Epimerase 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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, ammonium acetate, Bis-Tris, ammonium ferric citrate, alpha ketoglutarate, sodium chloride
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.07→47.8 Å / Num. all: 379883 / Num. obs: 76968 / % possible obs: 99.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.7
Reflection shellResolution: 2.07→2.13 Å / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 1.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble of 2opw, 2a1x, 2fct

2opw

2a1x

2fct


Resolution: 2.13→47.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.825 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20312 3557 5 %RANDOM
Rwork0.17585 ---
obs0.17725 67031 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.491 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0.46 Å2
2--2.28 Å20 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.13→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7565 0 48 457 8070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197836
X-RAY DIFFRACTIONr_bond_other_d0.0120.027375
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.97310690
X-RAY DIFFRACTIONr_angle_other_deg1.961316926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2135996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03721.496341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.484151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8391590
X-RAY DIFFRACTIONr_chiral_restr0.110.21185
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218908
X-RAY DIFFRACTIONr_gen_planes_other0.010.021798
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_it2.0122.6053979
X-RAY DIFFRACTIONr_mcbond_other2.0022.6043977
X-RAY DIFFRACTIONr_mcangle_it3.213.8844961
X-RAY DIFFRACTIONr_mcangle_other3.2113.8854962
X-RAY DIFFRACTIONr_scbond_it2.5192.9483857
X-RAY DIFFRACTIONr_scbond_other2.5192.9493858
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0844.2965725
X-RAY DIFFRACTIONr_long_range_B_refined7.67721.8058842
X-RAY DIFFRACTIONr_long_range_B_other7.6321.4048673
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)
11A288040.08
12B288040.08
21A276400.08
22C276400.08
31A279640.08
32D279640.08
41B275100.09
42C275100.09
51B278260.08
52D278260.08
61C278820.08
62D278820.08
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 262 -
Rwork0.314 4966 -
obs--99.11 %
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)
11.99650.54270.25111.43480.0392.0506-0.01110.10210.0529-0.20910.0398-0.0935-0.06230.0152-0.02880.0447-0.00560.04110.18890.02730.072454.57.459112.626
21.3560.3667-0.11412.23790.44842.09240.0547-0.033-0.0614-0.0425-0.10580.22860.011-0.12910.05120.0434-0.00620.03960.212-0.01710.091535.151-12.69592.219
33.2257-0.36550.70891.5508-0.47423.52520.0122-0.3359-0.19010.17730.01230.05840.2351-0.34-0.02450.0533-0.02850.02650.20430.03150.065229.409-2.68140.575
42.5584-0.0726-0.43081.6021-0.10373.29370.0440.28810.3173-0.0047-0.0812-0.0571-0.35790.17040.03730.127-0.01280.01540.30910.07280.108340.91611.439166.986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 279
2X-RAY DIFFRACTION2B17 - 273
3X-RAY DIFFRACTION3C17 - 272
4X-RAY DIFFRACTION4D17 - 272

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