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- PDB-6kfw: The cytochrome P450 enzyme CxnD for C-S bond formation in chuangx... -

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Basic information

Entry
Database: PDB / ID: 6kfw
TitleThe cytochrome P450 enzyme CxnD for C-S bond formation in chuangxinmycin biosynthesis
ComponentsCxnD
KeywordsOXIDOREDUCTASE / P450 / CxnD
Function / homologyChem-D8L / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesActinoplanes tsinanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHong, B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: The Cytochrome P450 Catalyzing C-S Bond Formation in S-Heterocyclization of Chuangxinmycin Biosynthesis.
Authors: Shi, Y. / Jiang, Z. / Hu, X. / Hu, X. / Gu, R. / Jiang, B. / Zuo, L. / Li, X. / Sun, H. / Zhang, C. / Wang, L. / Wu, L. / Hong, B.
History
DepositionJul 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 9, 2022Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CxnD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5136
Polymers45,3731
Non-polymers1,1405
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-39 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.460, 76.291, 80.029
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein CxnD


Mass: 45372.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes tsinanensis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-D8L / (2R)-3-(1H-indol-3-yl)-2-methylsulfanyl-propanoic acid


Mass: 235.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29784 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.051 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1312 / Rpim(I) all: 0.198 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHW

2whw


Resolution: 2→25.88 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.4137 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2383 1474 4.97 %
Rwork0.1823 28156 -
obs0.1851 29630 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.96 Å2
Refinement stepCycle: LAST / Resolution: 2→25.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 74 278 3521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01713322
X-RAY DIFFRACTIONf_angle_d2.58784540
X-RAY DIFFRACTIONf_chiral_restr0.2368508
X-RAY DIFFRACTIONf_plane_restr0.0103590
X-RAY DIFFRACTIONf_dihedral_angle_d19.11581248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.24481290.21042424X-RAY DIFFRACTION95.8
2.06-2.140.23441290.18942543X-RAY DIFFRACTION100
2.14-2.220.24361160.172563X-RAY DIFFRACTION100
2.22-2.320.22291150.16652552X-RAY DIFFRACTION100
2.32-2.450.24221350.17772548X-RAY DIFFRACTION100
2.45-2.60.23841400.17852548X-RAY DIFFRACTION100
2.6-2.80.26231450.18592560X-RAY DIFFRACTION100
2.8-3.080.27291390.19832574X-RAY DIFFRACTION99.96
3.08-3.530.22521630.18622554X-RAY DIFFRACTION99.89
3.53-4.440.21341540.16392605X-RAY DIFFRACTION99.6
4.44-25.880.2511090.19152685X-RAY DIFFRACTION97.28

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