[English] 日本語
Yorodumi
- PDB-5dyp: Crystal structure of Asp251Gly/Gln307His mutant of cytochrome P450 BM3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dyp
TitleCrystal structure of Asp251Gly/Gln307His mutant of cytochrome P450 BM3
ComponentsBifunctional P-450/NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / cytochrome P450 / random mutagenesis / drug metabolism
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 / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / 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. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDi Nardo, G. / Dell'Angelo, V. / Gilardi, G.
CitationJournal: Arch.Biochem.Biophys. / Year: 2016
Title: Subtle structural changes in the Asp251Gly/Gln307His P450 BM3 mutant responsible for new activity toward diclofenac, tolbutamide and ibuprofen.
Authors: Di Nardo, G. / Dell'Angelo, V. / Catucci, G. / Sadeghi, S.J. / Gilardi, G.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional P-450/NADPH-P450 reductase
C: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4154
Polymers107,1822
Non-polymers1,2332
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-42 kcal/mol
Surface area36690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.134, 118.448, 146.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3


Mass: 53591.078 Da / Num. of mol.: 2 / Mutation: D251G, Q307H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / Production host: Escherichia coli (E. coli)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 14% PEG 3350, 100 mM cacodylic acid pH 5.5-6.8, 100-160 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→48.98 Å / Num. obs: 41881 / % possible obs: 98.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.6 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPZ

1jpz


Resolution: 2.4→47 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 2071 4.95 %Random selection
Rwork0.2201 ---
obs0.2219 41824 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 0 86 148 7411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067443
X-RAY DIFFRACTIONf_angle_d1.22810079
X-RAY DIFFRACTIONf_dihedral_angle_d14.8572797
X-RAY DIFFRACTIONf_chiral_restr0.0451078
X-RAY DIFFRACTIONf_plane_restr0.0061301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45590.34891500.31232644X-RAY DIFFRACTION99
2.4559-2.51730.40241200.30662654X-RAY DIFFRACTION100
2.5173-2.58530.33991460.29772626X-RAY DIFFRACTION99
2.5853-2.66140.31991440.29772637X-RAY DIFFRACTION99
2.6614-2.74730.34181420.29172630X-RAY DIFFRACTION99
2.7473-2.84550.3231310.27912640X-RAY DIFFRACTION99
2.8455-2.95940.371200.2782675X-RAY DIFFRACTION99
2.9594-3.09410.25651350.27052637X-RAY DIFFRACTION99
3.0941-3.25710.34971490.25722637X-RAY DIFFRACTION99
3.2571-3.46110.2831320.24232646X-RAY DIFFRACTION99
3.4611-3.72830.28661400.21932634X-RAY DIFFRACTION98
3.7283-4.10330.21771510.18992633X-RAY DIFFRACTION97
4.1033-4.69660.20471260.17072664X-RAY DIFFRACTION97
4.6966-5.91530.19131440.1882653X-RAY DIFFRACTION97
5.9153-47.0030.21061410.18012743X-RAY DIFFRACTION95
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)
13.36531.3401-0.68555.5911-0.80270.73360.148-0.6654-0.12370.38210.0977-0.21870.51840.1975-0.19160.608-0.1295-0.12160.76870.04280.44521.49236.15063.2966
22.7458-0.48482.22421.5031-0.04965.16580.42750.1943-0.1123-0.04180.1034-0.5256-0.10340.7267-0.39390.2541-0.10090.05340.5294-0.17670.583911.642120.3354-19.0083
34.4655-1.35553.52520.7042-0.20316.16881.4762-0.2244-1.650.00790.1549-0.50532.64121.0403-1.05821.21360.0283-0.33071.1947-0.3511.307911.51057.9723-28.8295
42.59050.07742.0141.91680.28874.49870.2138-0.10410.22590.0140.0657-0.2631-0.34950.3028-0.20160.2816-0.08840.11210.4874-0.19330.4674.587124.9687-15.18
53.64061.3780.80941.58661.73465.1223-0.38780.5183-0.8783-0.81920.2912-0.4487-0.21750.17120.10890.8758-0.14340.2390.3757-0.11280.6713-10.97980.0429-76.2341
65.92241.2181.83262.26211.9635.402-0.0962-0.2078-0.2828-0.70080.10060.1155-0.8551-0.1511-0.07930.77920.02010.08390.33890.0210.427-8.621217.2622-55.6097
71.93010.55290.96592.21811.93.791-0.41830.3647-0.1812-0.86530.5925-0.4668-1.21630.8475-0.10821.0358-0.36520.30620.6392-0.05370.52330.334714.3927-70.7694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 225 )
4X-RAY DIFFRACTION4chain 'A' and (resid 226 through 455 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 93 )
6X-RAY DIFFRACTION6chain 'C' and (resid 94 through 311 )
7X-RAY DIFFRACTION7chain 'C' and (resid 312 through 456 )

+
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