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- PDB-5cwe: Structure of CYP107L2 from Streptomyces avermitilis with lauric acid -

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Basic information

Entry
Database: PDB / ID: 5cwe
TitleStructure of CYP107L2 from Streptomyces avermitilis with lauric acid
ComponentsCytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / Streptomyces avermitilis / P450 / CYP107L2 / lauric acid
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
LAURIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesStreptomyces avermitilis MA-4680 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsPham, T.-V. / Han, S.-H. / Kim, J.-H. / Kim, D.-H. / Kang, L.-W.
CitationJournal: To Be Published
Title: Structure of CYP107L2 from Streptomyces avermitilis with lauric acid
Authors: Pham, T.-V. / Han, S.-H. / Kim, J.-H. / Kim, D.-H. / Kang, L.-W.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 hydroxylase
B: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2789
Polymers86,3602
Non-polymers1,9187
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-93 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.080, 118.371, 66.039
Angle α, β, γ (deg.)90.00, 105.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 hydroxylase


Mass: 43180.176 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Lithium sulfate monohydrate, Tris-HCL, PEG 3350

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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: 2.39→50 Å / Num. obs: 37158 / % possible obs: 99.4 % / Redundancy: 4 % / Net I/σ(I): 25.5
Reflection shellResolution: 2.39→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata processing
MOLREPmodel building
PHASERphasing
HKL-2000data processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CD8

2cd8


Resolution: 2.39→47.43 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.865 / SU B: 12.525 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30085 1862 5 %RANDOM
Rwork0.22586 ---
obs0.22961 35267 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.737 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20.02 Å2
2---0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.39→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 130 168 6370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196345
X-RAY DIFFRACTIONr_bond_other_d0.0020.026102
X-RAY DIFFRACTIONr_angle_refined_deg1.7272.0158661
X-RAY DIFFRACTIONr_angle_other_deg1.071314004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19922.254284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0815986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9341576
X-RAY DIFFRACTIONr_chiral_restr0.1020.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217136
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021396
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_it3.0374.3843142
X-RAY DIFFRACTIONr_mcbond_other3.0364.3843141
X-RAY DIFFRACTIONr_mcangle_it4.7036.5713924
X-RAY DIFFRACTIONr_mcangle_other4.7036.5713925
X-RAY DIFFRACTIONr_scbond_it2.9674.5933203
X-RAY DIFFRACTIONr_scbond_other2.9644.5933203
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6196.7644738
X-RAY DIFFRACTIONr_long_range_B_refined7.25634.5787308
X-RAY DIFFRACTIONr_long_range_B_other7.25534.5797309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 125 -
Rwork0.332 2347 -
obs--88.48 %

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