[English] 日本語
Yorodumi
- PDB-7wdd: Crystal structure of the P450 BM3 heme domain mutant F87K in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / HYDROXYAMINE / Chem-IC6 / ethenylbenzene / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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

-
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)109,75113
Polymers106,8222
Non-polymers2,92911
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-41 kcal/mol
Surface area35160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.820, 148.836, 65.336
Angle α, β, γ (deg.)90.000, 100.090, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 through 4 and (name N...
21(chain B and (resid 3 through 12 or (resid 13...

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
11LYSLYSGLUGLU(chain A and ((resid 3 through 4 and (name N...AA3 - 45 - 6
12ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
13ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
14ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
15ILEILELEULEU(chain A and ((resid 3 through 4 and (name N...AA2 - 4554 - 457
21LYSLYSGLYGLY(chain B and (resid 3 through 12 or (resid 13...BB3 - 125 - 14
22GLUGLUGLUGLU(chain B and (resid 3 through 12 or (resid 13...BB1315
23LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457
24LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457
25LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457
26LYSLYSLEULEU(chain B and (resid 3 through 12 or (resid 13...BB3 - 4555 - 457

-
Components

-
Protein , 1 types, 2 molecules AB

#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

-
Non-polymers , 5 types, 259 molecules

#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-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3NO / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-SYN / ethenylbenzene / styrene


Mass: 104.149 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, 0.38 M MgCl2, 12-18% PEG3350 / PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.21→74.42 Å / Num. obs: 53101 / % possible obs: 96.6 % / Redundancy: 3.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.084 / Net I/σ(I): 6.2 / Num. measured all: 178933 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.21-2.333.50.4652495271360.840.2870.5482.488.8
7-74.423.40.041571616800.9950.0260.04910.893.3

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EGN

7egn


Resolution: 2.21→39.72 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 3676 3.79 %
Rwork0.1971 93342 -
obs0.1982 53058 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.35 Å2 / Biso mean: 50.8113 Å2 / Biso min: 26.3 Å2
Refinement stepCycle: final / Resolution: 2.21→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 210 248 7348
Biso mean--45.57 49.98 -
Num. residues----880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2674X-RAY DIFFRACTION5.432TORSIONAL
12B2674X-RAY DIFFRACTION5.432TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.240.34081390.29893567370689
2.24-2.270.3772920.31592304239657
2.27-2.310.31261490.27883769391895
2.31-2.340.26621530.27953896404995
2.34-2.380.31981470.26183759390695
2.38-2.420.2791490.24783818396794
2.42-2.460.32261490.25433830397995
2.46-2.50.26921500.24083785393594
2.5-2.550.23161450.24263721386694
2.55-2.60.2341500.24083813396394
2.6-2.660.3051500.23683800395094
2.66-2.720.2691450.24963753389894
2.72-2.790.29061450.2273708385393
2.79-2.860.25311410.22883710385192
2.86-2.950.23721430.23643702384591
2.95-3.040.27621430.2333539368289
3.04-3.150.24441370.22883531366888
3.15-3.280.30531380.22253618375688
3.28-3.430.24031410.21423488362987
3.43-3.610.21231350.18523475361086
3.61-3.830.19931420.1783416355885
3.83-4.130.17811380.16333469360786
4.13-4.550.1761360.13933459359586
4.55-5.20.18281340.14693401353585
5.2-6.550.20041430.18473485362886
6.55-39.720.18461420.15843526366888
Refinement TLS params.Method: refined / Origin x: -5.2343 Å / Origin y: -12.1337 Å / Origin z: 0.3703 Å
111213212223313233
T0.321 Å20.0013 Å20.0013 Å2-0.316 Å20.0116 Å2--0.3153 Å2
L0.1979 °20.1651 °20.0911 °2-0.4035 °20.3366 °2--0.2869 °2
S0.0002 Å °0.0271 Å °0.0064 Å °-0.0272 Å °0.0203 Å °-0.0158 Å °-0.0351 Å °0.0156 Å °-0.018 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 455
2X-RAY DIFFRACTION1allA501 - 801
3X-RAY DIFFRACTION1allB3 - 455
4X-RAY DIFFRACTION1allB501 - 1101
5X-RAY DIFFRACTION1allS1 - 254

+
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://pdbjlvh1.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