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- PDB-9bat: Crystal structure of sterol 14 alpha-demethylase (CYP51) from dee... -

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Basic information

Entry
Database: PDB / ID: 9bat
TitleCrystal structure of sterol 14 alpha-demethylase (CYP51) from deep-sea fish Coryphaenoides armatus (abyssal grenadier) in the ligand-free state
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / CYTOCHROME P450 / ENDOPLASMIC RETICULUM / STEROL BIOSYNTHESIS
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesCoryphaenoides armatus (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Minasov, G. / Lepesheva, G.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM067871 United States
CitationJournal: Int J Mol Sci / Year: 2025
Title: Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone.
Authors: Hargrove, T.Y. / Lamb, D.C. / Wawrzak, Z. / Minasov, G. / Goldstone, J.V. / Kelly, S.L. / Stegeman, J.J. / Lepesheva, G.I.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3064
Polymers102,0732
Non-polymers1,2332
Water39622
1
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6532
Polymers51,0371
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6532
Polymers51,0371
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.596, 63.135, 104.860
Angle α, β, γ (deg.)90.00, 97.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lanosterol 14-alpha demethylase


Mass: 51036.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coryphaenoides armatus (fish) / Gene: CYP51, ERG11 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: PEG 3350, Magnesium Acetate, Tetradecyl-b-D-maaltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→29.09 Å / Num. obs: 18679 / % possible obs: 96.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Χ2: 1.849 / Net I/σ(I): 27
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1073 / CC1/2: 0.786 / CC star: 0.938 / Rpim(I) all: 0.328 / Rrim(I) all: 0.799 / Χ2: 1.118 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.09 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU B: 19.922 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24817 996 5.1 %RANDOM
Rwork0.23173 ---
obs0.2329 18679 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.001 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å2-3.66 Å2
2--2.67 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: 1 / Resolution: 2.9→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 86 22 7127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127333
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166941
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.6849957
X-RAY DIFFRACTIONr_angle_other_deg0.371.58616005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5045880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.781552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.801101265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0510.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028566
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021718
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_it7.4669.8643532
X-RAY DIFFRACTIONr_mcbond_other7.4669.8643532
X-RAY DIFFRACTIONr_mcangle_it11.51817.7344408
X-RAY DIFFRACTIONr_mcangle_other11.51717.7344409
X-RAY DIFFRACTIONr_scbond_it7.52210.0093801
X-RAY DIFFRACTIONr_scbond_other7.52310.013799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.75518.2785549
X-RAY DIFFRACTIONr_long_range_B_refined16.5992.978108
X-RAY DIFFRACTIONr_long_range_B_other16.59192.978109
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 68 -
Rwork0.3 1381 -
obs--98.1 %

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