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- PDB-5gnm: Cytochrome P450 Vdh (CYP107BR1) L348M mutant -

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Basic information

Entry
Database: PDB / ID: 5gnm
TitleCytochrome P450 Vdh (CYP107BR1) L348M mutant
ComponentsVitamin D(3) 25-hydroxylase
KeywordsOXIDOREDUCTASE / cytochrome P450
Function / homology
Function and homology information


cholestanetriol 26-monooxygenase / cholestanetetraol 26-dehydrogenase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / 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 / Vitamin D(3) 25-hydroxylase
Similarity search - Component
Biological speciesPseudonocardia autotrophica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYasutake, Y. / Tamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
NEDO Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structural insights into the mechanism of the drastic changes in enzymatic activity of the cytochrome P450 vitamin D3 hydroxylase (CYP107BR1) caused by a mutation distant from the active site
Authors: Yasutake, Y. / Kameda, T. / Tamura, T.
History
DepositionJul 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D(3) 25-hydroxylase
B: Vitamin D(3) 25-hydroxylase
C: Vitamin D(3) 25-hydroxylase
D: Vitamin D(3) 25-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,4898
Polymers182,0234
Non-polymers2,4664
Water2,378132
1
A: Vitamin D(3) 25-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1222
Polymers45,5061
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area17470 Å2
MethodPISA
2
B: Vitamin D(3) 25-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1222
Polymers45,5061
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-25 kcal/mol
Surface area17110 Å2
MethodPISA
3
C: Vitamin D(3) 25-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1222
Polymers45,5061
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-25 kcal/mol
Surface area17410 Å2
MethodPISA
4
D: Vitamin D(3) 25-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1222
Polymers45,5061
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-26 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.220, 107.650, 88.360
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Vitamin D(3) 25-hydroxylase / Cytochrome P450 / CYP107BR1


Mass: 45505.645 Da / Num. of mol.: 4 / Mutation: L348M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia autotrophica (bacteria) / Gene: vdh / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)-RIL
References: UniProt: C4B644, cholestanetriol 26-monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-tris, 100 mM NaCl, 50 mM CaCl2, 22-24% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.641
11-h,-k,l20.359
ReflectionResolution: 2.7→50 Å / Num. obs: 41314 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 8.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A4G

3a4g


Resolution: 2.7→45.97 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.843 / SU B: 28.679 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27494 2091 5.1 %RANDOM
Rwork0.22298 ---
obs0.22563 39203 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.475 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å27.43 Å2
2--1.47 Å20 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.7→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12386 0 172 132 12690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01912850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3272.00417542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76951596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84123.217572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.795152082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.89715128
X-RAY DIFFRACTIONr_chiral_restr0.0810.21964
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219876
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_it0.1080.6966396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.2011.0437988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.070.7186454
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined1.4725.97919171
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.692→2.762 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.526 134 -
Rwork0.435 2541 -
obs--86.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44270.0315-0.92240.81240.01331.6261-0.00710.1525-0.0513-0.10850.03070.08440.1019-0.1161-0.02360.1442-0.0043-0.13020.2723-0.01610.12199.7809-0.64816.5925
20.91570.26330.3661.25420.01511.33240.0268-0.12020.03560.1103-0.0370.0347-0.0479-0.0050.01020.09420.0035-0.07320.253-0.00740.073150.18170.87637.7629
30.78-0.12340.14861.3160.17731.42440.02270.05330.0084-0.136-0.0345-0.0806-0.03640.03990.01180.1132-0.0034-0.08220.24980.01330.087846.68980.7406-6.4725
40.92840.1058-0.48590.8006-0.0171.71460.026-0.1096-0.06050.0918-0.0202-0.08070.03780.0477-0.00580.18330.0068-0.16080.31340.00670.14286.1867-0.3126-27.4496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 401
2X-RAY DIFFRACTION2B3 - 401
3X-RAY DIFFRACTION3C3 - 403
4X-RAY DIFFRACTION4D3 - 403

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