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- PDB-8w6z: Substrate-bound crystal structure of a P450 enzyme DmlH that cata... -

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Basic information

Entry
Database: PDB / ID: 8w6z
TitleSubstrate-bound crystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins
Components
  • Cytochrome P450
  • THR-D4P-GLU-GLY-BB8-PRO-KJW-GLY-A1D5P-DPN
KeywordsBIOSYNTHETIC PROTEIN / P450 enzyme / intramolecular phenol coupling / cihanmycins
Function / homology: / PROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesStreptomyces sp. DM14 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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: To Be Published
Title: Substrate-bound crystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins
Authors: Fang, C. / Zhang, L. / Zhu, Y. / Zhang, C.
History
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 2.0Jun 19, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_entry_details.compound_details ..._atom_site.auth_seq_id / _pdbx_entry_details.compound_details / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
B: THR-D4P-GLU-GLY-BB8-PRO-KJW-GLY-A1D5P-DPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9944
Polymers48,0862
Non-polymers9082
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-39 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.082, 100.162, 105.811
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: Protein/peptide THR-D4P-GLU-GLY-BB8-PRO-KJW-GLY-A1D5P-DPN


Type: Cyclic peptide / Class: Unknown / Mass: 1227.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. DM14 (bacteria) / References: BIRD: PRD_002429
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-R8L / (E)-3-[2-[(2R,3S)-3-[(1R)-1-aminocarbonyloxypropyl]oxiran-2-yl]phenyl]prop-2-enoic acid


Type: Cyclic peptide / Class: Unknown / Mass: 291.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17NO5 / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002429
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAuthor stated that they first isolated this compound from the Streptomyces lividans SBT18 host ...Author stated that they first isolated this compound from the Streptomyces lividans SBT18 host haboring the biosynthetic gene cluster of cihanmycin (GenBank accession no.TQJ01344-TQJ01379), with the cytochrome p450 monooxygenase gene cih33 inactivated.
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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19.68 Å / Num. obs: 20263 / % possible obs: 99.9 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.032 / Rrim(I) all: 0.101 / Net I/σ(I): 15.8 / Num. measured all: 188014
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.49 / Num. measured all: 14569 / Num. unique obs: 2903 / CC1/2: 0.828 / Rpim(I) all: 0.24 / Rrim(I) all: 0.548 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
MOLREPphasing
CrysalisPro171.39.7edata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.68 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 949 4.7 %
Rwork0.183 --
obs0.1854 20211 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 150 193 3384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083266
X-RAY DIFFRACTIONf_angle_d0.9344451
X-RAY DIFFRACTIONf_dihedral_angle_d9.07535
X-RAY DIFFRACTIONf_chiral_restr0.052491
X-RAY DIFFRACTIONf_plane_restr0.014596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.25531400.19532692X-RAY DIFFRACTION100
2.32-2.460.25571390.19652700X-RAY DIFFRACTION100
2.46-2.650.23991190.19272713X-RAY DIFFRACTION100
2.65-2.920.2631260.20012724X-RAY DIFFRACTION100
2.92-3.340.24711350.1882759X-RAY DIFFRACTION100
3.34-4.20.22461370.16742765X-RAY DIFFRACTION100
4.2-19.680.20631530.1752909X-RAY DIFFRACTION100

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