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- PDB-7wdi: Crystal structure of the P450 BM3 heme domain mutant F87K in comp... -

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Basic information

Entry
Database: PDB / ID: 7wdi
TitleCrystal structure of the P450 BM3 heme domain mutant F87K in complex with N-imidazolyl-hexanoyl-L-phenylalanine and hydroxylamine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Dual-functional small molecule / P450 heme domain / Complex
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROXYAMINE / Chem-IC6 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJiang, Y. / Dong, S. / Feng, Y. / Cong, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778060 China
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: To Be Published
Title: Crystal structure of the P450 BM3 heme domain mutant F87A in complex with N-imidazolyl-hexanoyl-L-phenylalanine and hydroxylamine
Authors: Jiang, Y. / Cong, Z.
History
DepositionDec 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,43810
Polymers106,8222
Non-polymers2,6178
Water14,178787
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-43 kcal/mol
Surface area33990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.413, 149.017, 65.281
Angle α, β, γ (deg.)90.000, 100.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 185 or (resid 186...
21(chain B and (resid 2 through 173 or (resid 174...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEMETMET(chain A and (resid 2 through 185 or (resid 186...AA2 - 1854 - 187
12ASNASNLYSLYS(chain A and (resid 2 through 185 or (resid 186...AA186 - 187188 - 189
13ILEILELEULEU(chain A and (resid 2 through 185 or (resid 186...AA2 - 4554 - 457
14ILEILELEULEU(chain A and (resid 2 through 185 or (resid 186...AA2 - 4554 - 457
15ILEILELEULEU(chain A and (resid 2 through 185 or (resid 186...AA2 - 4554 - 457
16ILEILELEULEU(chain A and (resid 2 through 185 or (resid 186...AA2 - 4554 - 457
21ILEILEPHEPHE(chain B and (resid 2 through 173 or (resid 174...BB2 - 1734 - 175
22ILEILEILEILE(chain B and (resid 2 through 173 or (resid 174...BB174176
23ILEILELEULEU(chain B and (resid 2 through 173 or (resid 174...BB2 - 4554 - 457
24ILEILELEULEU(chain B and (resid 2 through 173 or (resid 174...BB2 - 4554 - 457
25ILEILELEULEU(chain B and (resid 2 through 173 or (resid 174...BB2 - 4554 - 457
26ILEILELEULEU(chain B and (resid 2 through 173 or (resid 174...BB2 - 4554 - 457

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Components

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase


Mass: 53410.859 Da / Num. of mol.: 2 / Mutation: F87K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IC6 / (2S)-2-(6-imidazol-1-ylhexanoylamino)-3-phenyl-propanoic acid


Mass: 329.394 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 0.38 M MgCl2, 12-18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 63293 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.061 / Rrim(I) all: 0.115 / Χ2: 0.879 / Net I/σ(I): 5.5 / Num. measured all: 214546
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.40.55131510.7050.3470.6530.63899.1
2.14-2.183.40.48731780.7560.3060.5770.70299.2
2.18-2.223.40.41731260.7950.2640.4950.71899.3
2.22-2.263.40.36531720.8380.230.4320.75499.2
2.26-2.313.40.3431310.8550.2160.4040.77499.1
2.31-2.373.20.29331620.870.1920.3510.79799.5
2.37-2.4230.25631700.8870.1760.3120.85898.2
2.42-2.493.40.23331400.9110.1490.2770.89199.7
2.49-2.563.60.21431760.9320.1320.2520.90599.8
2.56-2.653.60.18931890.9420.1170.2230.93499.8
2.65-2.743.60.17431450.9470.1080.2050.96499.5
2.74-2.853.50.14331470.9610.090.171.0199.4
2.85-2.983.50.13131770.9640.0820.1550.99899.5
2.98-3.143.50.11331570.9710.070.1331.06398.8
3.14-3.333.30.09631610.9760.0620.1141.08299
3.33-3.592.90.08231410.980.0570.11.14498.2
3.59-3.953.50.07531830.9840.0470.0881.03399.7
3.95-4.523.50.06531860.9880.0410.0760.9299.8
4.52-5.73.40.06331840.9860.040.0750.83299.3
5.7-503.30.05532170.9930.0350.0650.57498.7

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EGN

7egn


Resolution: 2.1→29.25 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 1999 3.24 %
Rwork0.1835 59662 -
obs0.1846 61661 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.72 Å2 / Biso mean: 30.7157 Å2 / Biso min: 11.78 Å2
Refinement stepCycle: final / Resolution: 2.1→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6939 0 186 787 7912
Biso mean--20.75 36.89 -
Num. residues----883
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2670X-RAY DIFFRACTION3.476TORSIONAL
12B2670X-RAY DIFFRACTION3.476TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.25051080.2183218332673
2.15-2.210.27251330.2243962409590
2.21-2.270.27251420.21784240438296
2.27-2.350.26931440.21444310445497
2.35-2.430.24971450.21554323446898
2.43-2.530.23931470.20384392453999
2.53-2.640.25931470.196744114558100
2.64-2.780.2241480.19284395454399
2.78-2.960.21871470.19314407455499
2.96-3.180.2411470.18974370451799
3.18-3.50.1991470.17934378452599
3.5-4.010.18681470.15824409455699
4.01-5.050.17111490.144244294578100
5.05-29.250.22261480.18584418456698

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