[English] 日本語
Yorodumi
- PDB-5yqa: The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yqa
TitleThe crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / metabolites biosynthesis / catabolism Cytoplasm
Function / homology
Function and homology information


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, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-propylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsZhou, W. / Zhang, T. / Qiao, R. / Bell, S. / Coleman, T.
CitationJournal: To Be Published
Title: The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid
Authors: Coleman, T. / Zhang, T. / Qiao, R. / Zhou, W. / Beii, S.
History
DepositionNov 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4044
Polymers44,5871
Non-polymers8163
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-37 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.860, 51.377, 79.588
Angle α, β, γ (deg.)90.00, 92.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44587.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2IU02
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-8ZU / 4-propylbenzoic acid


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.25M NaCl, 1.5M (NH4)2SO4, 0.1M Bis-Tris, pH 8.0

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 72080 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.6
Reflection shellResolution: 1.38→1.4 Å

-
Processing

Software
NameVersionClassification
PHENIX1.6.2_432refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNZ

4dnz


Resolution: 1.38→33.345 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.96
RfactorNum. reflection% reflection
Rfree0.1961 3485 5.06 %
Rwork0.1785 --
obs0.1794 68855 94.52 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 42.379 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3474 Å2-0 Å20.228 Å2
2---0.9499 Å20 Å2
3----0.3974 Å2
Refinement stepCycle: LAST / Resolution: 1.38→33.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 56 475 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063178
X-RAY DIFFRACTIONf_angle_d1.1554347
X-RAY DIFFRACTIONf_dihedral_angle_d12.7611174
X-RAY DIFFRACTIONf_chiral_restr0.074473
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3799-1.39880.27041070.2111944X-RAY DIFFRACTION71
1.3988-1.41880.25071150.20762189X-RAY DIFFRACTION79
1.4188-1.440.24271050.20542387X-RAY DIFFRACTION86
1.44-1.46250.24241380.19972448X-RAY DIFFRACTION89
1.4625-1.48650.23911220.18862548X-RAY DIFFRACTION94
1.4865-1.51210.21581380.18262635X-RAY DIFFRACTION94
1.5121-1.53960.19781520.17932583X-RAY DIFFRACTION95
1.5396-1.56920.22261260.17612678X-RAY DIFFRACTION95
1.5692-1.60130.19221420.17392623X-RAY DIFFRACTION96
1.6013-1.63610.19131240.17242671X-RAY DIFFRACTION97
1.6361-1.67410.19881510.16572653X-RAY DIFFRACTION97
1.6741-1.7160.19231460.16452689X-RAY DIFFRACTION97
1.716-1.76240.19271470.16582709X-RAY DIFFRACTION98
1.7624-1.81420.19211390.1662689X-RAY DIFFRACTION98
1.8142-1.87280.18381600.16982661X-RAY DIFFRACTION97
1.8728-1.93970.20121480.16892729X-RAY DIFFRACTION99
1.9397-2.01740.2091430.16942741X-RAY DIFFRACTION99
2.0174-2.10920.19551510.17082737X-RAY DIFFRACTION99
2.1092-2.22040.17441560.17042725X-RAY DIFFRACTION99
2.2204-2.35940.21331210.17072766X-RAY DIFFRACTION99
2.3594-2.54150.19651610.18092734X-RAY DIFFRACTION99
2.5415-2.79720.21111660.19982718X-RAY DIFFRACTION98
2.7972-3.20170.20321470.19172765X-RAY DIFFRACTION99
3.2017-4.03270.16951500.17442639X-RAY DIFFRACTION95
4.0327-33.3550.18161300.17952709X-RAY DIFFRACTION94

+
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