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- PDB-8z9s: Substrate-free structure of CYP105AW5 from deep-sea Streptomyces ... -

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Basic information

Entry
Database: PDB / ID: 8z9s
TitleSubstrate-free structure of CYP105AW5 from deep-sea Streptomyces aculeolatus
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / CYP105 / hydroxylase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesStreptomyces aculeolatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsGao, Q. / Yang, J. / Xu, L.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Substrate-free structure of CYP105AW5 from deep-sea Streptomyces aculeolatus
Authors: Gao, Q. / Yang, J. / Xu, L.H.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5116
Polymers45,4701
Non-polymers1,0415
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.840, 140.330, 48.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450


Mass: 45469.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aculeolatus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 510 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.06 M divalent cations (0.3 M magnesium chloride hexahydrate and 0.3 M calcium chloride dehydrate), 0.1 M Buffer system 2 (1 M sodium HEPES and MOPS, pH 7.5) and 50% (v/v) Precipitant Mix 1 ...Details: 0.06 M divalent cations (0.3 M magnesium chloride hexahydrate and 0.3 M calcium chloride dehydrate), 0.1 M Buffer system 2 (1 M sodium HEPES and MOPS, pH 7.5) and 50% (v/v) Precipitant Mix 1 [40% (v/v) PEG 500 MME and 20% (w/v) PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.69→40.59 Å / Num. obs: 58251 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Net I/σ(I): 16.9
Reflection shellResolution: 1.69→1.73 Å / Num. unique obs: 4220 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→40.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.826 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20142 1945 3.4 %RANDOM
Rwork0.16724 ---
obs0.16843 54863 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.679 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.69→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 71 505 3771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133333
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173168
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.6734548
X-RAY DIFFRACTIONr_angle_other_deg1.5081.587301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49620.632190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88215524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681537
X-RAY DIFFRACTIONr_chiral_restr0.1020.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023765
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1372.1441655
X-RAY DIFFRACTIONr_mcbond_other2.1282.1421654
X-RAY DIFFRACTIONr_mcangle_it3.0253.2092067
X-RAY DIFFRACTIONr_mcangle_other3.0283.212068
X-RAY DIFFRACTIONr_scbond_it3.8752.611678
X-RAY DIFFRACTIONr_scbond_other3.8742.6111679
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7883.7182482
X-RAY DIFFRACTIONr_long_range_B_refined7.04828.5473962
X-RAY DIFFRACTIONr_long_range_B_other6.89927.3593793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 135 -
Rwork0.218 3725 -
obs--90.72 %

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