[English] 日本語
Yorodumi
- PDB-7y9l: Crystal structure of P450 BM3-2F from Bacillus megaterium in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y9l
TitleCrystal structure of P450 BM3-2F from Bacillus megaterium in complex with 2-Hydroxy-5-Nitrobenzonitrile
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / synthesis / monooxygenase
Function / homology
Function and homology information


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 / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...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 / aromatase activity / metabolic process / response to hormone / 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
5-nitro-2-oxidanyl-benzenecarbonitrile / PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWang, Q. / Zhang, L.L. / Liu, W.D. / Huang, J.-W. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: to be published
Title: Crystal structure of P450 BM3-2F from Bacillus megaterium in complex with 2-Hydroxy-5-Nitrobenzonitrile
Authors: Wang, Q. / Zhang, L.L. / Liu, W.D. / Huang, J.-W. / Yang, Y. / Chen, C.-C. / Guo, R.-T.
History
DepositionJun 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4908
Polymers104,8112
Non-polymers1,6796
Water12,322684
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2454
Polymers52,4061
Non-polymers8393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-21 kcal/mol
Surface area19110 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2454
Polymers52,4061
Non-polymers8393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-21 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.014, 146.956, 63.271
Angle α, β, γ (deg.)90.000, 98.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 52 or resid 54...
21(chain B and (resid 5 through 40 or (resid 41...

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
11METMETLEULEU(chain A and (resid 5 through 52 or resid 54...AA5 - 525 - 52
12SERSERLEULEU(chain A and (resid 5 through 52 or resid 54...AA54 - 26254 - 262
13ALAALATHRTHR(chain A and (resid 5 through 52 or resid 54...AA264 - 269264 - 269
14GLYGLYGLNGLN(chain A and (resid 5 through 52 or resid 54...AA271 - 403271 - 403
15PHEPHELEULEU(chain A and (resid 5 through 52 or resid 54...AA405 - 455405 - 455
166VP6VP6VP6VP(chain A and (resid 5 through 52 or resid 54...AC1001
21METMETPHEPHE(chain B and (resid 5 through 40 or (resid 41...BB5 - 405 - 40
22LYSLYSLYSLYS(chain B and (resid 5 through 40 or (resid 41...BB4141
23METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
24METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
25METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
26METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
27METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
28METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455
29METMETLEULEU(chain B and (resid 5 through 40 or (resid 41...BB5 - 4555 - 455

-
Components

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


Mass: 52405.730 Da / Num. of mol.: 2 / Mutation: A82F,A328F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria)
Strain: ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19
Gene: cyp102A1, cyp102, BG04_163 / Plasmid: pRSF-DuetI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical ChemComp-6VP / 5-nitro-2-oxidanyl-benzenecarbonitrile / 2-hydroxy-5-nitrobenzonitrile


Mass: 164.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25-30% PEG 3350, 0.1 M MgCl2, 0.1 M HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→25 Å / Num. obs: 100707 / % possible obs: 95.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.055 / Χ2: 1.981 / Net I/σ(I): 19.3 / Num. measured all: 530937
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.824.80.42993460.8570.2140.4810.90289.3
1.82-1.95.50.30395420.9420.1390.3341.0391.1
1.9-1.985.50.21498120.9730.0960.2351.18193.1
1.98-2.095.40.14299930.9860.0650.1561.41295.2
2.09-2.225.40.104101240.9920.0480.1151.67396.4
2.22-2.395.30.083102230.9950.0390.0922.10497.3
2.39-2.635.30.067103060.9960.0320.0742.48797.9
2.63-3.015.20.053103880.9970.0250.0592.79598.5
3.01-3.795.10.041104720.9980.020.0452.97999.3
3.79-255.20.038105010.9980.0180.0423.04498.6

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPA

4kpa


Resolution: 1.76→24.78 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 2012 2 %
Rwork0.173 98598 -
obs0.1736 100610 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.19 Å2 / Biso mean: 36.5465 Å2 / Biso min: 17.14 Å2
Refinement stepCycle: final / Resolution: 1.76→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7250 0 112 684 8046
Biso mean--26.29 42.83 -
Num. residues----896
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2694X-RAY DIFFRACTION6.016TORSIONAL
12B2694X-RAY DIFFRACTION6.016TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.820.25272010.239073927489
1.82-1.90.22241890.20219345953491
1.9-1.980.22781770.19789639981693
1.98-2.090.24292130.188397881000195
2.09-2.220.23972030.182999101011396
2.22-2.390.21111960.1784100361023297
2.39-2.630.22322030.181101041030798
2.63-3.010.21362110.1855101721038399
3.01-3.790.19082110.164102601047199
3.79-24.780.17822080.1562102711047998

+
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