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- PDB-8w72: Crystal structure of a P450 enzyme DmlH that catalyze intramolecu... -

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Basic information

Entry
Database: PDB / ID: 8w72
TitleCrystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins
ComponentsCytochrome P450
KeywordsBIOSYNTHETIC PROTEIN / P450 enzyme / intramolecular phenol coupling / cihanmycins
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStreptomyces sp. DM14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsFang, C. / Zhang, L. / Zhu, Y. / Zhang, C.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22177118 China
National Natural Science Foundation of China (NSFC)31820103003 China
National Natural Science Foundation of China (NSFC)31630004 China
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Discovery and Biosynthesis of Cihanmycins Reveal Cytochrome P450-Catalyzed Intramolecular C-O Phenol Coupling Reactions.
Authors: Fang, C. / Zhang, L. / Wang, Y. / Xiong, W. / Yan, Z. / Zhang, W. / Zhang, Q. / Wang, B. / Zhu, Y. / Zhang, C.
History
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4752
Polymers46,8591
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-25 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.333, 100.440, 106.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450


Mass: 46858.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. DM14 (bacteria)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 40.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.3 M CaCl2, 0.3 M MgCl2, 0.5 M MES, 0.5 M imidazole, 37.5% w/v PEG 1K_PEG 3350_MPD, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.25→53.49 Å / Num. obs: 6132 / % possible obs: 92.4 % / Redundancy: 7.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.058 / Rrim(I) all: 0.162 / Χ2: 0.93 / Net I/σ(I): 9.5 / Num. measured all: 45745
Reflection shellResolution: 3.25→3.43 Å / % possible obs: 91.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.541 / Num. measured all: 3695 / Num. unique obs: 844 / CC1/2: 0.805 / Rpim(I) all: 0.26 / Rrim(I) all: 0.605 / Χ2: 0.75 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→50.22 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3028 292 4.79 %
Rwork0.2027 --
obs0.2072 6093 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→50.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 43 0 3034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113099
X-RAY DIFFRACTIONf_angle_d1.3384220
X-RAY DIFFRACTIONf_dihedral_angle_d8.414437
X-RAY DIFFRACTIONf_chiral_restr0.063471
X-RAY DIFFRACTIONf_plane_restr0.012557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-4.10.32151330.21982591X-RAY DIFFRACTION85
4.1-50.220.29381590.19533210X-RAY DIFFRACTION100

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