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- PDB-5zis: Crystal structure of Mn-ProtoporphyrinIX-reconstituted P450BM3 -

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Basic information

Entry
Database: PDB / ID: 5zis
TitleCrystal structure of Mn-ProtoporphyrinIX-reconstituted P450BM3
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450
Function / homology
Function and homology information


aromatase activity / NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein 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 / Cytochrome p450 / Cytochrome P450 / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...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 / Cytochrome p450 / Cytochrome P450 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MANGANESE PROTOPORPHYRIN IX / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsOmura, K. / Aiba, Y. / Onoda, H. / Sugimoto, H. / Shoji, O. / Watanabe, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR15P3 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H03087 Japan
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: Reconstitution of full-length P450BM3 with an artificial metal complex by utilising the transpeptidase Sortase A.
Authors: Omura, K. / Aiba, Y. / Onoda, H. / Stanfield, J.K. / Ariyasu, S. / Sugimoto, H. / Shiro, Y. / Shoji, O. / Watanabe, Y.
History
DepositionMar 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
C: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,1408
Polymers208,6784
Non-polymers2,4624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-76 kcal/mol
Surface area71210 Å2
Unit cell
Length a, b, c (Å)104.760, 155.320, 208.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Bifunctional cytochrome P450/NADPH--P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3


Mass: 52169.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512) (bacteria)
Strain: ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512
Gene: cyp102A1, cyp102, BG04_163 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical
ChemComp-MNH / MANGANESE PROTOPORPHYRIN IX


Mass: 615.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32MnN4O4

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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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M magnesium chloride, 12% PEG 3350, 0.1 M MES buffer (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→46.83 Å / Num. obs: 30923 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 88.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.053 / Rrim(I) all: 0.145 / Net I/σ(I): 9.9 / Num. measured all: 225247 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.1-3.277.41.21644420.580.4741.30698.9
9.8-46.836.70.03910630.9980.0160.04398.5

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
Aimless0.6.2data scaling
PHENIX1.13refinement
PDB_EXTRACT3.24data extraction
MOLREP11.6.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAG

1fag


Resolution: 3.1→19.929 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.18
RfactorNum. reflection% reflection
Rfree0.29 1566 5.09 %
Rwork0.2577 --
obs0.2594 30757 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 240.56 Å2 / Biso mean: 100.2412 Å2 / Biso min: 39.32 Å2
Refinement stepCycle: final / Resolution: 3.1→19.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14550 0 172 0 14722
Biso mean--64.19 --
Num. residues----1804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.19970.40131380.368925812719
3.1997-3.31350.40491490.362626292778
3.3135-3.44560.41561380.35326312769
3.4456-3.60150.36541250.351726702795
3.6015-3.79020.38921370.325126172754
3.7902-4.02580.32561430.292126292772
4.0258-4.33370.2951420.269726392781
4.3337-4.76440.26371390.23226572796
4.7644-5.44150.26231450.238226712816
5.4415-6.810.30561580.251926852843
6.81-19.9290.19851520.183127822934
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.36841.51181.90471.25970.65082.864-0.5807-1.3401-0.081-0.25630.00510.2481-0.7423-0.93630.42040.69330.43620.03660.95290.13970.774730.883626.05795.7424
22.9655-0.121.74831.8251-0.03084.6214-0.4519-0.7391-0.00160.7007-0.09360.0586-0.2525-0.17050.58510.88370.5007-0.01031.2824-0.13560.768231.250732.565820.7437
34.21360.74432.73442.24881.29653.1535-0.7322-0.1989-0.0805-0.66690.39550.1172-1.05230.29150.22840.84070.050.03710.64570.14790.526539.274729.8496-1.4215
40.95180.40620.0111.9620.51122.76590.1671-0.4766-0.16660.3008-0.2075-0.2271-0.2208-0.2712-0.04660.7158-0.1274-0.1380.95120.06040.609277.648337.93350.7397
51.19020.0967-0.57041.37481.46391.80580.1407-0.0246-0.1684-0.269-0.26110.0607-0.0429-0.56050.1020.73240.0238-0.09220.84020.12880.520463.862634.461930.6607
61.0881-0.55040.46331.88820.06382.7408-0.0930.00760.2496-0.5503-0.0948-0.0463-0.6522-0.04660.01840.95450.0159-0.02560.53250.08880.840970.885447.355829.0283
72.1745-0.2105-0.06422.14620.45082.1870.0825-0.56710.5430.1426-0.1783-0.1331-0.8574-0.1573-0.0410.929-0.03470.00050.7439-0.10270.596567.857850.476444.5582
81.9567-0.0574-0.84640.69910.97172.95510.1995-0.3553-0.18220.5324-0.16780.06091.0054-0.8432-0.28520.8882-0.2064-0.17430.912-0.07540.635636.4978-0.782732.8429
95.55390.17660.63051.6563-0.45122.74320.3855-0.1445-0.77110.09890.1231-0.16220.39240.2332-0.34250.74250.0341-0.27430.2953-0.04050.648758.9105-1.810325.2812
103.07320.1286-1.67611.2023-0.1436-0.62530.0979-0.6816-0.65330.3729-0.1449-0.33450.911-0.49790.00351.229-0.108-0.41180.65470.1330.964549.0396-12.102333.9559
111.40630.13390.61861.60460.17751.7781-0.4132-0.03530.62260.11590.0571-0.0554-0.22910.47650.28920.64310.0128-0.06221.25830.13451.1426110.314627.96530.9743
122.72731.19351.5841.88080.53582.67040.3012-0.12520.17670.0469-0.19210.10860.15110.2207-0.0590.6080.2616-0.19780.7535-0.1320.832892.69327.818833.3843
133.5831.36220.52213.04280.32692.03180.3088-0.4426-0.26170.75680.11410.12640.86940.1149-0.33350.7370.3968-0.15820.7174-0.15450.766494.78184.046939.1062
142.03750.0529-1.8112.6812-0.04692.71150.32810.80810.0274-0.2614-0.2072-0.41570.32151.0173-0.04070.63610.4073-0.16171.2227-0.06180.8394105.380611.62219.6939
152.4646-0.205-0.83151.6325-0.29161.2752-0.09160.93330.1329-0.14850.3867-0.4453-0.0270.6089-0.24330.72520.4006-0.11911.1769-0.22960.802297.659711.628716.4208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 158 )A4 - 158
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 250 )A159 - 250
3X-RAY DIFFRACTION3chain 'A' and (resid 251 through 455 )A251 - 455
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 108 )B6 - 108
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 224 )B109 - 224
6X-RAY DIFFRACTION6chain 'B' and (resid 225 through 312 )B225 - 312
7X-RAY DIFFRACTION7chain 'B' and (resid 313 through 454 )B313 - 454
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 108 )C4 - 108
9X-RAY DIFFRACTION9chain 'C' and (resid 109 through 324 )C109 - 324
10X-RAY DIFFRACTION10chain 'C' and (resid 325 through 455 )C325 - 455
11X-RAY DIFFRACTION11chain 'D' and (resid 5 through 72 )D5 - 72
12X-RAY DIFFRACTION12chain 'D' and (resid 73 through 198 )D73 - 198
13X-RAY DIFFRACTION13chain 'D' and (resid 199 through 282 )D199 - 282
14X-RAY DIFFRACTION14chain 'D' and (resid 283 through 362 )D283 - 362
15X-RAY DIFFRACTION15chain 'D' and (resid 363 through 455 )D363 - 455

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