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- PDB-4r82: Streptomyces globisporus C-1027 NADH:FAD oxidoreductase SgcE6 in ... -

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Basic information

Entry
Database: PDB / ID: 4r82
TitleStreptomyces globisporus C-1027 NADH:FAD oxidoreductase SgcE6 in complex with NAD and FAD fragments
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


FAD reductase (NADH) / pyrimidine nucleobase catabolic process / riboflavin reductase (NADPH) activity / antibiotic biosynthetic process / FMN binding
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH-dependent FAD reductase
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.659 Å
AuthorsTan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...Tan, K. / Bigelow, L. / Clancy, S. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor ...Title: Crystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier Protein-Tethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C-1027 in Streptomyces globisporus.
Authors: Chang, C.Y. / Lohman, J.R. / Cao, H. / Tan, K. / Rudolf, J.D. / Ma, M. / Xu, W. / Bingman, C.A. / Yennamalli, R.M. / Bigelow, L. / Babnigg, G. / Yan, X. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references / Structure summary
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,61418
Polymers39,9382
Non-polymers4,67616
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-91 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.046, 62.830, 70.089
Angle α, β, γ (deg.)90.00, 92.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Oxidoreductase


Mass: 19968.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8GME2

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Non-polymers , 7 types, 252 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M calcium acetate, 0.1M MES:NaCl, 20% (w/v) PEG8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.66→35 Å / Num. all: 43097 / Num. obs: 43097 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.7 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.6
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2 / Num. unique all: 2089 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.659→34.928 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 2168 5.04 %random
Rwork0.1631 ---
obs0.1644 43034 99.38 %-
all-43034 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.659→34.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 176 236 2882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062752
X-RAY DIFFRACTIONf_angle_d1.1583772
X-RAY DIFFRACTIONf_dihedral_angle_d12.838944
X-RAY DIFFRACTIONf_chiral_restr0.078422
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6587-1.69730.26871190.24452653X-RAY DIFFRACTION96
1.6973-1.73970.22341590.19582678X-RAY DIFFRACTION99
1.7397-1.78680.21231480.18312712X-RAY DIFFRACTION100
1.7868-1.83930.23131470.17792732X-RAY DIFFRACTION100
1.8393-1.89870.19121290.17562750X-RAY DIFFRACTION100
1.8987-1.96660.20781380.16512703X-RAY DIFFRACTION100
1.9666-2.04530.17211670.16372713X-RAY DIFFRACTION100
2.0453-2.13840.1761500.15852720X-RAY DIFFRACTION100
2.1384-2.25110.18071530.16042721X-RAY DIFFRACTION100
2.2511-2.39210.20131610.15892711X-RAY DIFFRACTION100
2.3921-2.57670.21781270.1642758X-RAY DIFFRACTION100
2.5767-2.83590.18541360.16972769X-RAY DIFFRACTION100
2.8359-3.24610.20841320.15932758X-RAY DIFFRACTION100
3.2461-4.08870.18021530.14552715X-RAY DIFFRACTION99
4.0887-34.93550.15111490.15792773X-RAY DIFFRACTION98
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)
11.0957-0.1263-0.35380.6480.16321.56510.00820.009-0.0457-0.0487-0.0360.0473-0.0252-0.15810.01390.1041-0.0019-0.01230.0814-0.00670.117112.1960.750810.6163
21.28970.0551-0.6061.7449-0.24111.41160.00220.076-0.0272-0.16760.00660.02920.0126-0.08460.0230.1104-0.0033-0.03770.0898-0.01140.106519.13092.29115.2865
31.697-0.0228-0.80260.90960.08611.78560.0061-0.0914-0.09240.04920.0421-0.06190.01530.189-0.05120.10710.0038-0.02290.0999-0.00540.116523.46692.613521.0954
43.0434-2.066-0.88815.1498-1.27012.2528-0.1829-0.5165-0.26920.22850.35320.1280.3136-0.0977-0.11380.2372-0.0107-0.02770.19890.02540.13718.7988-0.692634.1689
52.36290.4240.23273.96530.15113.07130.0683-0.40360.09350.4420.0325-0.1114-0.08920.0745-0.0520.17060.01220.0030.1676-0.02640.094417.50811.41234.6799
62.8035-0.5278-0.45971.87430.01281.0830.0141-0.02140.0949-0.00180.01230.0928-0.0731-0.0811-0.03380.0963-0.0029-0.02770.1224-0.01870.031315.51987.87822.2622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 177 )
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 67 )
4X-RAY DIFFRACTION4chain 'B' and (resid 68 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 134 )
6X-RAY DIFFRACTION6chain 'B' and (resid 135 through 177 )

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