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- PDB-6hqd: Cytochrome P450-153 from Pseudomonas sp. 19-rlim -

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Basic information

Entry
Database: PDB / ID: 6hqd
TitleCytochrome P450-153 from Pseudomonas sp. 19-rlim
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome P450 / heme / biocatalysis / Cyp153 family / METAL BINDING PROTEIN
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 / TRIETHYLENE GLYCOL / S,R MESO-TARTARIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesPseudomonas sp. 19-rlim (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFiorentini, F. / Mattevi, A.
CitationJournal: Biochemistry / Year: 2018
Title: The Extreme Structural Plasticity in the CYP153 Subfamily of P450s Directs Development of Designer Hydroxylases.
Authors: Fiorentini, F. / Hatzl, A.M. / Schmidt, S. / Savino, S. / Glieder, A. / Mattevi, A.
History
DepositionSep 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,81613
Polymers145,0893
Non-polymers2,72610
Water5,783321
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2804
Polymers48,3631
Non-polymers9173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2224
Polymers48,3631
Non-polymers8593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3145
Polymers48,3631
Non-polymers9514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.311, 96.642, 87.777
Angle α, β, γ (deg.)90.00, 119.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Cytochrome P450 /


Mass: 48363.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. 19-rlim (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G3LGZ6

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Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 M diammonium tartrate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→44 Å / Num. obs: 116816 / % possible obs: 99.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.155 / Num. unique obs: 5829 / CC1/2: 0.544 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RWL

3rwl


Resolution: 1.8→44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.902 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20011 5690 4.9 %RANDOM
Rwork0.1698 ---
obs0.17133 111097 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0.5 Å2
2--0.56 Å20 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.8→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9929 0 176 321 10426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01410363
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179129
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.68314102
X-RAY DIFFRACTIONr_angle_other_deg0.9821.64621392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63451238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36920.925584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4651595
X-RAY DIFFRACTIONr_chiral_restr0.0780.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211677
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021927
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_it1.8782.3374961
X-RAY DIFFRACTIONr_mcbond_other1.8742.3364960
X-RAY DIFFRACTIONr_mcangle_it2.5133.4926196
X-RAY DIFFRACTIONr_mcangle_other2.5133.4926197
X-RAY DIFFRACTIONr_scbond_it3.0552.6865402
X-RAY DIFFRACTIONr_scbond_other3.0552.6865402
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5763.8897907
X-RAY DIFFRACTIONr_long_range_B_refined5.33526.95111142
X-RAY DIFFRACTIONr_long_range_B_other5.33826.93411121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 498 -
Rwork0.282 8217 -
obs--99.89 %

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