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- PDB-5cje: Structure of CYP107L2 -

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Basic information

Entry
Database: PDB / ID: 5cje
TitleStructure of CYP107L2
ComponentsCytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / Streptomyces avermitilis / P450 / CYP107L2
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
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 / Cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesStreptomyces avermitilis MA-4680 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPham, T.-V. / Han, S.-H. / Kim, J.-H. / Kim, D.-H. / Kang, L.-W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea2011-0016509 Korea, Republic Of
Cooperative Research Program for Agriculture Science & Technology DevelopmentPJ01127901 Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of CYP107L2
Authors: Pham, T.-V. / Han, S.-H. / Kim, J.-H. / Kim, D.-H. / Kang, L.-W.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8893
Polymers43,1801
Non-polymers7092
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-27 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.184, 50.585, 74.638
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

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Components

#1: Protein Cytochrome P450 hydroxylase / Cytochrome P450 107L2


Mass: 43180.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis MA-4680 (bacteria)
Strain: MA-4680 / Gene: cyp8, SAV_1987 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82LM3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: Sodium Citrate, Imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14255 / % possible obs: 99.2 % / Redundancy: 5.3 % / Net I/σ(I): 30.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 7.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHASERphasing
Cootmodel building
DENZOdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CD8

2cd8


Resolution: 2.5→36.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.747 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.765 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25545 713 5 %RANDOM
Rwork0.17016 ---
obs0.17435 13540 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.5→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 49 75 3134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193132
X-RAY DIFFRACTIONr_bond_other_d0.0020.023005
X-RAY DIFFRACTIONr_angle_refined_deg1.6242.0124281
X-RAY DIFFRACTIONr_angle_other_deg1.02136895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42122.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42415486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4941537
X-RAY DIFFRACTIONr_chiral_restr0.0860.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213532
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02689
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_it2.6253.9561559
X-RAY DIFFRACTIONr_mcbond_other2.6263.9561558
X-RAY DIFFRACTIONr_mcangle_it4.0055.9291947
X-RAY DIFFRACTIONr_mcangle_other4.0045.9291948
X-RAY DIFFRACTIONr_scbond_it3.3824.3561573
X-RAY DIFFRACTIONr_scbond_other3.3844.3571571
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4086.3672334
X-RAY DIFFRACTIONr_long_range_B_refined7.33231.5123528
X-RAY DIFFRACTIONr_long_range_B_other7.33231.5123528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 48 -
Rwork0.216 980 -
obs--96.53 %

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