[English] 日本語
Yorodumi
- PDB-5yhj: Cytochrome P450EX alpha (CYP152N1) wild-type with myristic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yhj
TitleCytochrome P450EX alpha (CYP152N1) wild-type with myristic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Fatty Acid Peroxygenase
Function / homology
Function and homology information


sterol metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MYRISTIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesExiguobacterium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOnoda, H. / Shoji, O. / Suzuki, K. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16J02846 Japan
The Ministry of Education,Culture,Sports,Science and Technology(MEXT)15H05806 Japan
The Ministry of Education,Culture,Sports,Science and Technology(MEXT)17H03087 Japan
CitationJournal: Catalysis Science And Technology / Year: 2017
Title: Alpha-Oxidative Decarboxylation of Fatty Acids Catalysed by Cytochrome P450 Peroxygenases Yielding Shorter-Alkyl-Chain Fatty Acids
Authors: Onoda, H. / Shoji, O. / Suzuki, K. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionSep 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0166
Polymers95,3262
Non-polymers1,6904
Water1,06359
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5083
Polymers47,6631
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5083
Polymers47,6631
Non-polymers8452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-48 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.962, 58.962, 238.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Cytochrome P450


Mass: 47663.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sp. (strain ATCC BAA-1283 / AT1b) (bacteria)
Strain: ATCC BAA-1283 / AT1b / Gene: EAT1b_2299 / Plasmid: pQE30t-CYP152N1
Details (production host): Thrombin_cleavage_site-BamHI-CYP152N1-ter-HindII
Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: C4L2G9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 uL Protein solution (16 mg/ml CYP152N1, 0.05 M MES buffer pH 7.0, 20% v/v Glycerol) and 1 uL (0.1M Tris-HCl buffer pH 8.5, 0.2M Magnesium chloride, 30% w/v polyethylene glycol 4000 (Pre- ...Details: 1 uL Protein solution (16 mg/ml CYP152N1, 0.05 M MES buffer pH 7.0, 20% v/v Glycerol) and 1 uL (0.1M Tris-HCl buffer pH 8.5, 0.2M Magnesium chloride, 30% w/v polyethylene glycol 4000 (Pre-Crystallization Test Reagent A2, Hampton Research)
PH range: 7.0-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 35823 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.95 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 1.094 / Net I/av σ(I): 29.79 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.70.335.0936220.9810.1360.3571.026100
2.38-2.486.80.2466.6235680.990.1020.2671.012100
2.48-2.596.80.1899.4235870.9940.0780.2051.094100
2.59-2.736.80.14611.7535630.9940.060.1581.071100
2.73-2.96.80.10815.4335920.9960.0450.1171.056100
2.9-3.126.80.07520.8236120.9980.0310.0811.04499.9
3.12-3.436.80.05329.2235740.9990.0220.0571.059100
3.43-3.936.80.0393836010.9990.0160.0421.15799.9
3.93-4.936.70.03145.7835960.9990.0130.0341.22899.4
4.93-206.60.03344.7135080.9990.0140.0361.19296.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.746 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.85
RfactorNum. reflection% reflection
Rfree0.2478 1986 5.56 %
Rwork0.2142 --
obs0.2161 35736 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.6 Å2 / Biso mean: 57.8494 Å2 / Biso min: 19.73 Å2
Refinement stepCycle: final / Resolution: 2.3→19.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 0 118 59 6834
Biso mean--49.89 42.99 -
Num. residues----817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096948
X-RAY DIFFRACTIONf_angle_d1.0489415
X-RAY DIFFRACTIONf_chiral_restr0.052995
X-RAY DIFFRACTIONf_plane_restr0.0061211
X-RAY DIFFRACTIONf_dihedral_angle_d17.5214122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2991-2.35650.3441410.27982425256699
2.3565-2.42010.31061390.265623682507100
2.4201-2.49120.29661400.248424282568100
2.4912-2.57150.35031510.239124172568100
2.5715-2.66320.27661420.240924172559100
2.6632-2.76950.28041430.240724012544100
2.7695-2.89520.3081410.237924242565100
2.8952-3.04730.23211420.234824042546100
3.0473-3.23750.29761380.230524462584100
3.2375-3.48620.24091460.228524272573100
3.4862-3.83470.26071400.202124072547100
3.8347-4.38430.19181390.182324352574100
4.3843-5.50380.21191420.1792410255299
5.5038-19.74650.22361420.20822341248396
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)
11.75570.6407-1.54790.80670.62733.8825-0.38730.5086-0.3384-0.04250.00830.08751.7018-0.61870.27840.7841-0.30390.06340.3981-0.06470.39284.84341.0395-17.7568
22.26482.0151-0.05942.5764-1.10156.0719-0.5039-0.6116-0.4629-0.29630.0911-0.11512.2515-0.44760.27881.1201-0.25060.23050.08560.06410.4665-0.7703-7.686610.0766
33.28021.0383-1.47220.611-0.20726.3164-0.34150.67410.2802-0.06130.35610.33970.3951-0.86230.06770.3044-0.1258-0.03120.32660.04220.3705-1.56939.5976-3.0726
43.91950.4386-1.77552.15830.5726.4323-0.1117-0.78540.14560.2313-0.13010.03450.49220.73670.23690.2413-0.0222-0.02630.3176-0.0170.336812.668613.962610.8509
51.42010.66490.65861.7215-1.51082.9189-0.05420.12050.03060.4126-0.3287-0.3455-0.60031.57920.28350.4216-0.2916-0.07420.8120.06560.426528.402624.5795-7.2575
62.72471.493-1.39643.1981-0.24885.99020.1338-0.5077-0.1943-0.2489-0.4343-0.6589-0.19172.15470.14540.1268-0.1390.03141.0340.1750.457135.574229.1856-33.9495
70.48830.9101-0.36083.2512-1.90296.09320.4082-0.12980.34840.769-0.37870.2941-1.0790.05950.03280.4312-0.12510.07420.2685-0.07160.392917.721932.1551-19.8939
82.6740.28581.09164.3142-2.01917.4402-0.05830.24610.1057-0.81440.00430.08150.67850.42180.16060.3214-0.01220.00430.3007-0.00530.315715.481416.7977-35.8816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 88 )A2 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 226 )A89 - 226
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 377 )A227 - 377
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 412 )A378 - 412
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 88 )B2 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 257 )B89 - 257
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 377 )B258 - 377
8X-RAY DIFFRACTION8chain 'B' and (resid 378 through 412 )B378 - 412

+
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