[English] 日本語
Yorodumi
- PDB-7wy3: Structure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wy3
TitleStructure of the Oxomolybdenum Mesoporphyrin IX-Reconstituted CYP102A1 F87V Mutant Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with Styrene
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Monooxygenase
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
Chem-GKX / Oxomolybdenum Mesoporphyrin IX / ethenylbenzene / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSuzuki, K. / Stanfield, J.K. / Shisaka, Y. / Omura, K. / Kasai, C. / Sugimoto, H. / Shoji, O.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR15P3 Japan
Japan Society for the Promotion of Science (JSPS)JP15H05806 Japan
Japan Society for the Promotion of Science (JSPS)JP18J23340 Japan
Japan Society for the Promotion of Science (JSPS)JP18J15250 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: A Compound I Mimic Reveals the Transient Active Species of a Cytochrome P450 Enzyme: Insight into the Stereoselectivity of P450-Catalysed Oxidations.
Authors: Suzuki, K. / Stanfield, J.K. / Omura, K. / Shisaka, Y. / Ariyasu, S. / Kasai, C. / Aiba, Y. / Sugimoto, H. / Shoji, O.
History
DepositionFeb 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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
Revision 1.4Nov 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)108,09024
Polymers104,5052
Non-polymers3,58522
Water8,791488
1
A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,04512
Polymers52,2531
Non-polymers1,79211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area19090 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,04512
Polymers52,2531
Non-polymers1,79211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.670, 128.380, 148.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 455 / Label seq-ID: 3 - 456

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 52252.617 Da / Num. of mol.: 2 / Mutation: F87V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium (bacteria) / Gene: BTA37_15100 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1Q8UP87, unspecific monooxygenase, NADPH-hemoprotein reductase

-
Non-polymers , 6 types, 510 molecules

#2: Chemical ChemComp-MI9 / Oxomolybdenum Mesoporphyrin IX


Mass: 676.613 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36MoN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GKX / (2~{S})-2-(5-cyclohexylpentanoylamino)-3-phenyl-propanoic acid


Mass: 331.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SYN / ethenylbenzene / styrene


Mass: 104.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: batch mode / Details: PEG8000, Magnesium Chloride, Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→48.58 Å / Num. obs: 148461 / % possible obs: 100 % / Redundancy: 9.794 % / Biso Wilson estimate: 31.613 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.144 / Χ2: 0.822 / Net I/σ(I): 8.08 / Num. measured all: 1454036 / Scaling rejects: 549
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.649.9122.0791.2310766510865108620.5542.19100
1.64-1.699.7981.671.4910373510587105870.6421.76100
1.69-1.749.5611.2761.929868810322103220.7531.347100
1.74-1.799.4290.9882.399460510034100330.8331.044100
1.79-1.859.4690.7593.0791727968896870.8910.802100
1.85-1.9110.0870.594.0195103942894280.9410.621100
1.91-1.9810.0610.4395.1591259907290710.9650.462100
1.98-2.0710.0190.3356.4987489873287320.9740.353100
2.07-2.169.7790.2617.8282577844484440.9850.276100
2.16-2.269.5390.219.2376704804180410.990.222100
2.26-2.399.6470.18110.5373938766476640.9920.191100
2.39-2.5310.3360.15812.0975177727372730.9940.166100
2.53-2.710.190.14313.2969549682568250.9930.151100
2.7-2.929.9740.12914.7163836640164000.9960.136100
2.92-3.29.3890.11815.7655262588658860.9960.125100
3.2-3.589.5920.10717.9151375535853560.9950.114100
3.58-4.1310.2270.09919.9448570474947490.9970.104100
4.13-5.069.820.08720.1539830405740560.9970.091100
5.06-7.169.1110.07918.6529100319431940.9970.083100
7.16-48.589.6420.05520.0317847185918510.9980.05999.6

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WSP

3wsp


Resolution: 1.6→48.58 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 4.413 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 7440 5 %RANDOM
Rwork0.1478 ---
obs0.1502 141021 99.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 183.78 Å2 / Biso mean: 30.556 Å2 / Biso min: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.71 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.6→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 250 488 8058
Biso mean--40.13 38.01 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177780
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.67411374
X-RAY DIFFRACTIONr_angle_other_deg1.3541.60418197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56151043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9123.597442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1291543
X-RAY DIFFRACTIONr_chiral_restr0.0770.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029394
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021683
X-RAY DIFFRACTIONr_rigid_bond_restr2.17316125
Refine LS restraints NCS

Ens-ID: 1 / Number: 16367 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 521 -
Rwork0.305 10325 -
all-10846 -
obs--99.92 %

+
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