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- PDB-4umz: PikC D50N mutant in complex with the engineered substrate mimic b... -

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Basic information

Entry
Database: PDB / ID: 4umz
TitlePikC D50N mutant in complex with the engineered substrate mimic bearing a 2-dimethylaminomethylbenzoate group
ComponentsCYTOCHROME P450 HYDROXYLASE PIKC
KeywordsELECTRON TRANSPORT / MONOOXYGENASE / PIKROMYCIN BIOSYNTHESIS
Function / homology
Function and homology information


pikromycin synthase / macrolide biosynthetic process / 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 / Chem-XJO / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesSTREPTOMYCES VENEZUELAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPodust, L.M. / Vieira, D.F.
CitationJournal: To be Published
Title: Recognition of Synthetic Substrates by P450 Pikc
Authors: Podust, L.M.
History
DepositionMay 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450 HYDROXYLASE PIKC
B: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6846
Polymers96,5362
Non-polymers2,1484
Water8,089449
1
A: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3423
Polymers48,2681
Non-polymers1,0742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3423
Polymers48,2681
Non-polymers1,0742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.061, 110.703, 151.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450 HYDROXYLASE PIKC


Mass: 48267.758 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: O87605
#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-XJO / (3R,4S,5S,7R,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 2-[(dimethylamino)methyl]benzoate


Mass: 457.602 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H39NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN CLEAVAGE SITE ARE FROM THE CLONING VECTOR ...FIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A D50N MUTATION IS ENGINEERED

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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: 2.69 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growpH: 5.6
Details: 4% TACSIMATE, PH 5.5, 16% PEG3350, 0.1M NA CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2014 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.32→151.62 Å / Num. obs: 40952 / % possible obs: 93.5 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.3
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VZM

2vzm


Resolution: 2.32→62.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.202 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24451 2069 5.1 %RANDOM
Rwork0.19004 ---
obs0.1928 38801 93.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.32→62.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 152 449 6695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196428
X-RAY DIFFRACTIONr_bond_other_d0.0010.026116
X-RAY DIFFRACTIONr_angle_refined_deg1.7692.0088808
X-RAY DIFFRACTIONr_angle_other_deg0.878313991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93222.34282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35515971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0991572
X-RAY DIFFRACTIONr_chiral_restr0.10.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217283
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021457
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_it2.5523.273172
X-RAY DIFFRACTIONr_mcbond_other2.553.2693171
X-RAY DIFFRACTIONr_mcangle_it4.0464.8953965
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0313.613256
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 93 -
Rwork0.27 1939 -
obs--63.88 %

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