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- PDB-3k9v: Crystal structure of rat mitochondrial P450 24A1 S57D in complex ... -

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Basic information

Entry
Database: PDB / ID: 3k9v
TitleCrystal structure of rat mitochondrial P450 24A1 S57D in complex with CHAPS
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 / vitamin D 25-hydroxylase activity / Vitamins / Vitamin D (calciferol) metabolism / 1-alpha,25-dihydroxyvitamin D3 23-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 / vitamin D 25-hydroxylase activity / Vitamins / Vitamin D (calciferol) metabolism / 1-alpha,25-dihydroxyvitamin D3 23-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: 2.5 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 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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)116,79010
Polymers111,8682
Non-polymers4,9228
Water4,774265
1
A: 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3955
Polymers55,9341
Non-polymers2,4614
Water181
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)58,3955
Polymers55,9341
Non-polymers2,4614
Water181
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)116,79010
Polymers111,8682
Non-polymers4,9228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1510 Å2
ΔGint-12 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.609, 81.647, 108.699
Angle α, β, γ (deg.)90.00, 122.89, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

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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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 3350, 0.1M Tris-HCl, 0.2 M potassium thiocyanate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→91.29 Å / Num. obs: 58240 / % possible obs: 98.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.598 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
PHASERphasing
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TQN

1tqn


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.334 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25154 2287 5 %RANDOM
Rwork0.20636 ---
obs0.20866 43128 97.44 %-
all-58240 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.342 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å21.41 Å2
2--1.07 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7594 0 298 265 8157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.98113848
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0027.51852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7123.722360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.209151460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8021560
X-RAY DIFFRACTIONr_chiral_restr0.0950.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219754
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6081.54652
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18227546
X-RAY DIFFRACTIONr_scbond_it1.51933446
X-RAY DIFFRACTIONr_scangle_it2.6274.53472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1856tight positional0.330.05
B1984loose positional0.775
A1856tight thermal4.150.5
B1984loose thermal4.0510
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 141 -
Rwork0.22 2617 -
obs--80.71 %

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