[English] 日本語
Yorodumi
- PDB-8q2f: Cytochrome P450 BM3 aMOx-A heme domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q2f
TitleCytochrome P450 BM3 aMOx-A heme domain
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450 monooxygenase / Anti-Markovnikov oxygenase
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 / 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 / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsKlaus, C. / Kowal, J.L. / Hammer, S.C. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)420112577 Germany
Citation
Journal: Chemrxiv / Year: 2024
Title: Directed Evolution Enables Dynamic Control of Transient Intermediates for Anti-Markovnikov Wacker-Tsuji-Type Oxidation of Unactivated Alkenes
Authors: Klaus, C. / Soler, J. / Kubik, G. / Gumulya, Y. / Hui, Y. / Watkins-Dulaney, E.J. / Heitland, ML. / Sommer, M. / Klein, A. / Kowal, J.L. / Niemann, H.H. / Arnold, F.H. / Garcia-Borras.M. / Hammer, S.C.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionAug 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
E: Bifunctional cytochrome P450/NADPH--P450 reductase
F: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,58653
Polymers325,5186
Non-polymers7,06847
Water00
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,03020
Polymers108,5062
Non-polymers2,52418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Bifunctional cytochrome P450/NADPH--P450 reductase
D: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,68115
Polymers108,5062
Non-polymers2,17513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Bifunctional cytochrome P450/NADPH--P450 reductase
F: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,87518
Polymers108,5062
Non-polymers2,36916
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.440, 167.440, 364.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0169568915392, 0.998936743713, -0.0428701048372), (-0.997837091677, 0.0196305774152, 0.0627357864674), (0.0635106471598, 0.0417135768039, 0.997109008688)47.9742252378, 52.2516590111, 6.85737131238
2given(0.0103370812904, -0.996726215393, 0.080187257709), (0.99978798146, 0.00887400193264, -0.018580748593), (0.0178083373444, 0.0803623272323, 0.996606622235)52.4253472076, -52.0322757751, -11.4383337624
3given(0.366333277622, -0.57431699316, 0.732092836377), (-0.677957536882, 0.374150033221, 0.632760089469), (-0.637317431027, -0.728128933643, -0.25229892608)74.4604189056, 34.5867860549, 60.6847175061
4given(-0.331842369184, 0.605006284479, -0.723773471298), (0.738797703766, -0.310394721878, -0.598191499054), (-0.586565081576, -0.733227462914, -0.343975133847)58.5790878394, -70.342111067, -25.6304052406
5given(0.302164837431, -0.623490231385, 0.72107998335), (0.724392046896, -0.341517984584, -0.598850255572), (0.619639067049, 0.703296095235, 0.348456638641)126.68832125, 15.4485829636, -47.1885036263

-
Components

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


Mass: 54253.023 Da / Num. of mol.: 6
Mutation: A44M, S72H, M77E, A78I, A82C, A87A, T88L, S89V, P142A, I174V, T175I, A184V, M212F, S226R, D232C, H236Q, E252G, Y256D, T269L, A290V, G315D, A328S, L353V, I366V, T372M, T436H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: cyp102A1, cyp102, BG04_163 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: reservoir solution: 2.4 M ammonium sulfate, 0.1 M MES pH 5.5, 5 mM magnesium acetate; protein solution: 9 mg/ml in 20 mM Tris pH 7.5, 200 mM NaCl; drop size: 200 nl protein + 100 nl reservoir

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.43→123.34 Å / Num. obs: 69594 / % possible obs: 97.94 % / Redundancy: 25.3 % / Biso Wilson estimate: 100.32 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.5703 / Rpim(I) all: 0.1134 / Rrim(I) all: 0.5818 / Net I/σ(I): 10.25
Reflection shellResolution: 3.43→3.553 Å / Redundancy: 9.3 % / Rmerge(I) obs: 2.99 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 6271 / CC1/2: 0.245 / Rrim(I) all: 3.153 / % possible all: 79.73

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Cootmodel building
PHENIXphasing
XDSVERSION Jan 10, 2022 BUILT=20220220data reduction
XDSVERSION Jan 10, 2022 BUILT=20220220data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.43→123.34 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 3444 5.01 %
Rwork0.1749 --
obs0.1774 68782 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.43→123.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22228 0 462 0 22690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423219
X-RAY DIFFRACTIONf_angle_d0.6631436
X-RAY DIFFRACTIONf_dihedral_angle_d11.8298763
X-RAY DIFFRACTIONf_chiral_restr0.0433328
X-RAY DIFFRACTIONf_plane_restr0.0054085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.43-3.480.427710.40691314X-RAY DIFFRACTION50
3.48-3.530.42351370.34172584X-RAY DIFFRACTION99
3.53-3.580.33351380.28852625X-RAY DIFFRACTION100
3.58-3.640.29561390.26262651X-RAY DIFFRACTION100
3.64-3.690.32941380.24212610X-RAY DIFFRACTION100
3.7-3.760.27791380.22722629X-RAY DIFFRACTION100
3.76-3.830.2591380.21292622X-RAY DIFFRACTION100
3.83-3.90.2491390.19872646X-RAY DIFFRACTION100
3.9-3.980.20871380.18752619X-RAY DIFFRACTION100
3.98-4.070.23951390.18312640X-RAY DIFFRACTION100
4.07-4.160.24011390.18372643X-RAY DIFFRACTION100
4.16-4.270.24121390.17332641X-RAY DIFFRACTION100
4.27-4.380.20421400.1652647X-RAY DIFFRACTION100
4.38-4.510.231390.14572657X-RAY DIFFRACTION100
4.51-4.660.17061400.1362645X-RAY DIFFRACTION100
4.66-4.820.21011390.14782651X-RAY DIFFRACTION100
4.82-5.010.22221400.152656X-RAY DIFFRACTION100
5.02-5.240.22181410.15742677X-RAY DIFFRACTION100
5.24-5.520.21921400.16442670X-RAY DIFFRACTION100
5.52-5.860.21591410.15862675X-RAY DIFFRACTION100
5.87-6.320.23581420.16372696X-RAY DIFFRACTION100
6.32-6.950.20531440.15952726X-RAY DIFFRACTION100
6.95-7.960.21611440.15172733X-RAY DIFFRACTION100
7.96-10.030.16451450.12532770X-RAY DIFFRACTION100
10.03-123.340.19681560.17982911X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more