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- PDB-5erl: Crystal structure of the epimerase SnoN in complex with Ni2+, suc... -

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Basic information

Entry
Database: PDB / ID: 5erl
TitleCrystal structure of the epimerase SnoN in complex with Ni2+, succinate and nogalamycin RO
ComponentsSnoN,SnoN
KeywordsISOMERASE / alpha ketoglutarate dependent epimerase / substrate complex / nogalamycin biosynthesis
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase 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 / NICKEL (II) ION / SUCCINIC ACID / SnoN / SnoN
Similarity search - Component
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Jan 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,SnoN
B: SnoN,SnoN
C: SnoN,SnoN
D: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,82216
Polymers132,3164
Non-polymers3,50612
Water27015
1
A: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9564
Polymers33,0791
Non-polymers8763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9564
Polymers33,0791
Non-polymers8763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9564
Polymers33,0791
Non-polymers8763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SnoN,SnoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9564
Polymers33,0791
Non-polymers8763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.324, 117.784, 160.964
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-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 / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA17 - 27129 - 283
21LEULEUBB17 - 27129 - 283
12ARGARGAA17 - 27329 - 285
22ARGARGCC17 - 27329 - 285
13ARGARGAA17 - 27229 - 284
23ARGARGDD17 - 27229 - 284
14LEULEUBB17 - 27129 - 283
24LEULEUCC17 - 27129 - 283
15LEULEUBB17 - 27129 - 283
25LEULEUDD17 - 27129 - 283
16ARGARGCC17 - 27229 - 284
26ARGARGDD17 - 27229 - 284

NCS ensembles :
ID
1
2
3
4
5
6

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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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#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.: 15 / 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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG3350, Bis-Tris, MgCl2, NiCl2, sodium succinate, nogalamycin RO
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.85→48.8 Å / Num. all: 32465 / Num. obs: 32465 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.5 / Num. measured all: 144964
Reflection shellResolution: 2.85→3 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

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

5ep9


Resolution: 2.85→48.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 40.736 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22417 1628 5.1 %RANDOM
Rwork0.20024 ---
obs0.20145 30530 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.152 Å2
Baniso -1Baniso -2Baniso -3
1-5.9 Å20 Å20 Å2
2--2.54 Å2-0 Å2
3----8.45 Å2
Refinement stepCycle: 1 / Resolution: 2.85→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7823 0 236 15 8074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198315
X-RAY DIFFRACTIONr_bond_other_d0.0090.027677
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.99811388
X-RAY DIFFRACTIONr_angle_other_deg1.9723.00917636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34651028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.46121.738351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.088151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7191587
X-RAY DIFFRACTIONr_chiral_restr0.1040.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0219305
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021854
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_it0.7641.3454112
X-RAY DIFFRACTIONr_mcbond_other0.7641.3444111
X-RAY DIFFRACTIONr_mcangle_it1.3962.0135134
X-RAY DIFFRACTIONr_mcangle_other1.3952.0145135
X-RAY DIFFRACTIONr_scbond_it1.291.4814203
X-RAY DIFFRACTIONr_scbond_other1.291.4824204
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2912.1946253
X-RAY DIFFRACTIONr_long_range_B_refined3.59212.1749205
X-RAY DIFFRACTIONr_long_range_B_other3.59212.1759206
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)
11A298000.04
12B298000.04
21A299280.05
22C299280.05
31A298940.04
32D298940.04
41B299880.03
42C299880.03
51B300080.02
52D300080.02
61C300840.03
62D300840.03
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 115 -
Rwork0.351 2069 -
obs--92.94 %
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)
13.26490.90810.35532.98191.05724.6866-0.0810.1390.1381-0.1615-0.13870.06210.1628-0.1610.21970.0211-0.01350.02170.68940.02860.596890.149136.777162.126
23.2085-0.09810.38691.5822-1.08886.4671-0.2615-0.4093-0.0690.78450.03640.3258-0.1961-0.99690.22520.4934-0.12660.24171.0272-0.10510.695178.255134.545198.648
32.5641-0.47560.6472.0677-0.58157.7550.25560.3386-0.2639-0.2961-0.3945-0.26030.24491.29940.1390.3654-0.03210.05951.12460.0570.7548109.473118.025203.007
41.58670.39520.85982.55760.10547.47780.1476-0.2026-0.26570.5152-0.25270.22322.2285-0.65950.10511.1118-0.45630.12540.9818-0.03680.763672.737105.759158.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 273
2X-RAY DIFFRACTION2B17 - 272
3X-RAY DIFFRACTION3C17 - 273
4X-RAY DIFFRACTION4D16 - 273

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