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- PDB-6hqg: Cytochrome P450-153 from Phenylobacterium zucineum -

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Basic information

Entry
Database: PDB / ID: 6hqg
TitleCytochrome P450-153 from Phenylobacterium zucineum
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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesPhenylobacterium zucineum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 25, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,9738
Polymers196,5074
Non-polymers2,4664
Water52229
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7432
Polymers49,1271
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7432
Polymers49,1271
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7432
Polymers49,1271
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7432
Polymers49,1271
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.464, 89.207, 201.820
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B1 - 999
2114A1 - 999
3114C1 - 999
4114D1 - 999

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.975596, -0.051333, 0.213488), (-0.050298, -0.998681, -0.010279), (0.213734, -0.00071, -0.976892)-31.88924, 92.89658, 295.23355
3given(0.506637, -0.848036, 0.155419), (-0.845323, -0.524056, -0.103893), (0.169553, -0.078743, -0.98237)38.4113, 127.18459, 303.23413
4given(0.594887, 0.803221, -0.030763), (-0.802288, 0.590973, -0.084173), (-0.04943, 0.074754, 0.995976)-11.0524, 75.98761, 0.67904

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Components

#1: Protein
Cytochrome P450


Mass: 49126.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phenylobacterium zucineum (strain HLK1) (bacteria)
Strain: HLK1 / Gene: p450, PHZ_c0813 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B4RGA3
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6 / Details: 0.1 M sodium citrate, 1 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.9→49.31 Å / Num. obs: 40389 / % possible obs: 97.6 % / Redundancy: 2.7 % / CC1/2: 0.964 / Rmerge(I) obs: 0.162 / Net I/σ(I): 5.4
Reflection shellResolution: 2.9→3.02 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4594 / CC1/2: 0.511 / % possible all: 98.3

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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: 2.9→49.31 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.85 / SU B: 22.512 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R Free: 0.454 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27172 2007 5 %RANDOM
Rwork0.21162 ---
obs0.21457 38381 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.642 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å2-0 Å20.93 Å2
2--0.29 Å20 Å2
3----2.17 Å2
Refinement stepCycle: 1 / Resolution: 2.9→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11886 0 172 29 12087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01412397
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710898
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.68816919
X-RAY DIFFRACTIONr_angle_other_deg0.8241.63625578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99551437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10620.924747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.712152045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.58515126
X-RAY DIFFRACTIONr_chiral_restr0.0680.21546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213939
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022297
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_it3.0924.1885790
X-RAY DIFFRACTIONr_mcbond_other3.094.1885789
X-RAY DIFFRACTIONr_mcangle_it4.9966.2687213
X-RAY DIFFRACTIONr_mcangle_other4.9966.2687214
X-RAY DIFFRACTIONr_scbond_it3.1754.4686607
X-RAY DIFFRACTIONr_scbond_other3.1764.4696605
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1476.5889706
X-RAY DIFFRACTIONr_long_range_B_refined7.49847.39613915
X-RAY DIFFRACTIONr_long_range_B_other7.49847.39513915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5681 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.210.5
Bmedium positional0.20.5
Cmedium positional0.210.5
Dmedium positional0.20.5
Amedium thermal7.732
Bmedium thermal5.772
Cmedium thermal9.472
Dmedium thermal5.972
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 156 -
Rwork0.359 2873 -
obs--98.38 %

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