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- PDB-3k9y: Crystal structure of rat mitochondrial P450 24A1 S57D in complex ... -

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Basic information

Entry
Database: PDB / ID: 3k9y
TitleCrystal structure of rat mitochondrial P450 24A1 S57D in complex with CYMAL-5
Components1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
KeywordsOXIDOREDUCTASE / MITOCHONDRIAL CYTOCHROME P450 / MONOTOPIC MEMBRANE PROTEIN / MONOOXYGENASE / VITAMIN D HORMONE METABOLISM / ADRENODOXIN
Function / homology
Function and homology information


vitamin D3 24-hydroxylase / 25-hydroxycholecalciferol-24-hydroxylase activity / 1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity / 25-hydroxycholecalciferol-23-hydroxylase activity / Vitamins / Vitamin D (calciferol) metabolism / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process ...vitamin D3 24-hydroxylase / 25-hydroxycholecalciferol-24-hydroxylase activity / 1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity / 25-hydroxycholecalciferol-23-hydroxylase activity / Vitamins / Vitamin D (calciferol) metabolism / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / vitamin D metabolic process / cellular response to vitamin D / response to vitamin D / osteoblast differentiation / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Cytochrome P450, E-class, CYP24A, mitochondrial / : / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAnnalora, A.J. / Goodin, D.B. / Hong, W. / Zhang, Q. / Johnson, E.F. / Stout, C.D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism.
Authors: Annalora, A.J. / Goodin, D.B. / Hong, W.X. / Zhang, Q. / Johnson, E.F. / Stout, C.D.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
B: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0906
Polymers111,8682
Non-polymers2,2224
Water00
1
A: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5394
Polymers55,9341
Non-polymers1,6063
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5502
Polymers55,9341
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
hetero molecules

B: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0906
Polymers111,8682
Non-polymers2,2224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4050 Å2
ΔGint-64 kcal/mol
Surface area40720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.297, 81.303, 108.707
Angle α, β, γ (deg.)90.00, 122.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial / Vitamin D(3) 24-hydroxylase / 24-OHase / Cytochrome P450 24A1 / P450-CC24


Mass: 55933.773 Da / Num. of mol.: 2 / Fragment: residues 34-514 / Mutation: S57D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cyp24, Cyp24a1 / Plasmid: pTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-FIQ
References: UniProt: Q09128, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 3350, 0.1 M Tris-HCl, 0.2M potassium thiocyanate, 0.05M CaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→91.67 Å / Num. all: 32727 / % possible obs: 97 % / Redundancy: 2.5 % / Biso Wilson estimate: 67.645 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.332 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1768 / Rsym value: 1.642 / % possible all: 70.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQN

1tqn


Resolution: 2.8→50 Å
RfactorNum. reflection% reflection
Rfree0.318 1619 -
Rwork0.251 --
all-32345 -
obs-30726 92.3 %
Displacement parametersBiso mean: 77.151 Å2
Baniso -1Baniso -2Baniso -3
1-1.045 Å20 Å2-18.334 Å2
2---13.505 Å20 Å2
3---12.46 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7549 0 154 0 7703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.605

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