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- PDB-4oo2: Streptomyces globisporus C-1027 FAD dependent (S)-3-chloro-β... -

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Basic information

Entry
Database: PDB / ID: 4oo2
TitleStreptomyces globisporus C-1027 FAD dependent (S)-3-chloro-β-tyrosine-S-SgcC2 C-5 hydroxylase SgcC apo form
ComponentsChlorophenol-4-monooxygenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Enzyme Discovery for Natural Product Biosynthesis / NatPro / putative HpaB-family monooxygenase / FAD binding / PSI-Biology
Function / homology
Function and homology information


(3S)-3-amino-3-(3-chloro-4-hydroxyphenyl)propanoyl-[peptidyl-carrier protein SgcC2] monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / antibiotic biosynthetic process / monooxygenase activity
Similarity search - Function
4-HPA 3-monooxygenase large component/Pyoverdin chromophore biosynthetic protein / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal ...4-HPA 3-monooxygenase large component/Pyoverdin chromophore biosynthetic protein / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(3S)-3-amino-3-(3-chloro-4-hydroxyphenyl)propanoyl-[peptidyl-carrier protein SgcC2] monooxygenase
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsCao, H. / Xu, W. / Bingman, C.A. / Lohman, J.R. / Yennamalli, R. / Shen, B. / Phillips Jr., G.N. / 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
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Structure summary
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Dec 7, 2016Group: Structure summary
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Mar 22, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _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_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorophenol-4-monooxygenase
B: Chlorophenol-4-monooxygenase
C: Chlorophenol-4-monooxygenase
D: Chlorophenol-4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,7177
Polymers235,5444
Non-polymers1723
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33820 Å2
ΔGint-194 kcal/mol
Surface area58370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.156, 173.729, 113.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chlorophenol-4-monooxygenase


Mass: 58886.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces globisporus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GMG6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 v/v mixture of SgcC (15mg/mL) with reservoir solution (Molecular Dimensions Morpheus screen A1 condition: 60mM mixture of MgCl2 and CaCl2; 100mM Imidazole and MES buffer pH 6.5; 30% ...Details: 1:1 v/v mixture of SgcC (15mg/mL) with reservoir solution (Molecular Dimensions Morpheus screen A1 condition: 60mM mixture of MgCl2 and CaCl2; 100mM Imidazole and MES buffer pH 6.5; 30% mixture of PEG550mme and PEG 20k), cryoprotected by Mitegen LV cryo-oil, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.91165 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 2.63→47.68 Å / Num. all: 113364 / Num. obs: 108116 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.75 % / Biso Wilson estimate: 39.95 Å2 / Rmerge(I) obs: 0.274 / Χ2: 1.211 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.63-2.810.0250.52742017261197
2.81-3.030.0250.934914319934196.8
3.03-3.320.0251.685168918490196.2
3.32-3.710.0253.244752016871195
3.71-4.280.0255.784259515135194
4.28-5.230.0257.93696913168193.5
5.23-7.350.0258.663119511102193.7
7.35-47.6750.02513.91245318605193
1367648101

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.14data extraction
JBluIce-EPICSdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→47.675 Å / SU ML: 0.44 / σ(F): 1.33 / Phase error: 27.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 3161 2.97 %Random
Rwork0.2166 ---
all0.2175 112884 --
obs0.2175 106551 94.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.02 Å2 / Biso mean: 56.9605 Å2 / Biso min: 27.23 Å2
Refinement stepCycle: LAST / Resolution: 2.63→47.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15842 0 8 217 16067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfhenix0.002
X-RAY DIFFRACTIONf_dihedral_angle_d18.859
LS refinement shellResolution: 2.63→2.67 Å
RfactorNum. reflection% reflection
Rfree0.36 177 -
Rwork0.38 --
obs-4028 86 %

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