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- PDB-4b7d: PikC bound to the 10-DML analog with the 3-(N,N-dimethylamino) pr... -

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Basic information

Entry
Database: PDB / ID: 4b7d
TitlePikC bound to the 10-DML analog with the 3-(N,N-dimethylamino) propanoate anchoring group
ComponentsCYTOCHROME P450 HYDROXYLASE PIKC
KeywordsOXIDOREDUCTASE / 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-QLE / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesSTREPTOMYCES VENEZUELAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsPodust, L.M.
CitationJournal: To be Published
Title: Recognition of Synthetic Substrates by P450 Pikc
Authors: Podust, L.M.
History
DepositionAug 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Non-polymer description
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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)98,8389
Polymers96,5372
Non-polymers2,3007
Water8,035446
1
A: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3734
Polymers48,2691
Non-polymers1,1043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450 HYDROXYLASE PIKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4655
Polymers48,2691
Non-polymers1,1964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.766, 58.042, 96.415
Angle α, β, γ (deg.)79.96, 79.52, 88.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CYTOCHROME P450 HYDROXYLASE PIKC / CYTOCHROME P450 MONOOXYGENASE


Mass: 48268.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THIOLATE LINK BETWEEN C 354 AND HEM 1407 / Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: O87605
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-QLE / [(3R,4S,5S,7R,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-bis(oxidanylidene)-1-oxacyclododec-9-en-4-yl] 3-(dimethylamino)propanoate


Mass: 395.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H37NO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN FE AND C 354 GLYCEROL (GOL): CRYO- ...PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND BETWEEN FE AND C 354 GLYCEROL (GOL): CRYO-PROTECTANT (3R,4S,5S,7R,11R,12R,E)-12-ETHYL-3,5,7,11-TETRAMETHYL-2, 8-DIOXOOXACYCLODODEC-9-EN-4-YL 3-(DIMETHYLAMINO)PROPANOATE (QLE): SYNTHETIC SUBSTRATE ANALOG
Sequence detailsFIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A

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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: 2.17 Å3/Da / Density % sol: 43.2 % / Description: NONE
Crystal growTemperature: 296 K / pH: 6.5
Details: 20% PEG 3350, 0.05 M AMMONIUM SULFATE, 0.1 M TRIS HCL, PH 6.5, 23 DEGREES C

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2012 / 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: 1.88→93.37 Å / Num. obs: 59193 / % possible obs: 94.2 % / Observed criterion σ(I): 1.4 / Redundancy: 1.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 7.8
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.4 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVJ

2bvj


Resolution: 1.89→93.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.947 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25747 2967 5.1 %RANDOM
Rwork0.19971 ---
obs0.20273 55068 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.07 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å2-0.91 Å2-0.17 Å2
2---1.33 Å20.88 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.89→93.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 160 446 6689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0462.0318803
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63322.226283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86315980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9881574
X-RAY DIFFRACTIONr_chiral_restr0.1370.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214984
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_it1.151.53968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90726381
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.30532462
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8234.52422
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: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 177 -
Rwork0.292 3791 -
obs--86.2 %

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