[English] 日本語
Yorodumi
- PDB-3pm0: Structural Characterization of the Complex between Alpha-Naphthof... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pm0
TitleStructural Characterization of the Complex between Alpha-Naphthoflavone and Human Cytochrome P450 1B1 (CYP1B1)
ComponentsCytochrome P450 1B1
KeywordsOXIDOREDUCTASE / CYP1B1 / P450 1B1 / P450 / MONOOXYGENASE / ALPHA-NAPHTHOFLAVONE / HEME / 17BETA-ESTRADIOL
Function / homology
Function and homology information


trabecular meshwork development / cellular response to cortisol stimulus / response to indole-3-methanol / Defective CYP1B1 causes Glaucoma / endothelial cell-cell adhesion / benzene-containing compound metabolic process / membrane lipid catabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / ganglion development ...trabecular meshwork development / cellular response to cortisol stimulus / response to indole-3-methanol / Defective CYP1B1 causes Glaucoma / endothelial cell-cell adhesion / benzene-containing compound metabolic process / membrane lipid catabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / ganglion development / retinal blood vessel morphogenesis / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / response to follicle-stimulating hormone / omega-hydroxylase P450 pathway / response to 3-methylcholanthrene / toxin metabolic process / epoxygenase P450 pathway / blood vessel endothelial cell migration / arachidonic acid metabolic process / cellular response to toxic substance / DNA modification / estrogen 16-alpha-hydroxylase activity / retinal metabolic process / cellular response to progesterone stimulus / cellular response to luteinizing hormone stimulus / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / sterol metabolic process / negative regulation of cell adhesion mediated by integrin / response to arsenic-containing substance / 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 / collagen fibril organization / blood vessel morphogenesis / regulation of reactive oxygen species metabolic process / estrogen metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / intrinsic apoptotic signaling pathway in response to oxidative stress / adrenal gland development / positive regulation of DNA biosynthetic process / negative regulation of NF-kappaB transcription factor activity / response to dexamethasone / positive regulation of smooth muscle cell migration / steroid metabolic process / cellular response to organic cyclic compound / estrous cycle / positive regulation of vascular endothelial growth factor production / endothelial cell migration / Endogenous sterols / cellular response to cAMP / nitric oxide biosynthetic process / monooxygenase activity / xenobiotic metabolic process / negative regulation of cell migration / response to nutrient / positive regulation of translation / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to hydrogen peroxide / positive regulation of angiogenesis / male gonad development / positive regulation of reactive oxygen species metabolic process / response to estradiol / cellular response to tumor necrosis factor / angiogenesis / cell adhesion / iron ion binding / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / mitochondrion
Similarity search - Function
Cytochrome P450, E-class, group I / 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
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 1B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, A. / Stout, C.D. / Johnson, E.F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Characterization of the Complex between {alpha}-Naphthoflavone and Human Cytochrome P450 1B1.
Authors: Wang, A. / Savas, U. / Stout, C.D. / Johnson, E.F.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7933
Polymers56,9041
Non-polymers8892
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.170, 103.980, 62.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Cytochrome P450 1B1 / CYPIB1


Mass: 56903.949 Da / Num. of mol.: 1 / Mutation: A119S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP1B1 / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / References: UniProt: Q16678, unspecific monooxygenase
#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-BHF / 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / 7,8-BENZOFLAVONE / ALPHA-NAPHTHOFLAVONE


Mass: 272.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS AMINO ACID SUBSTITUTION IS A NATURALLY OCCURRING ALLELIC VARIANT FOR THE ENZYME. IT ARISES ...THIS AMINO ACID SUBSTITUTION IS A NATURALLY OCCURRING ALLELIC VARIANT FOR THE ENZYME. IT ARISES FROM A SINGLE NUCLEOTIDE POLYMORPHISM (SNP) WHICH IS DESCRIBED IN THE SNP DATABASE WITH ACCESSION NUMBER RS1056827 WITH AN ALLELE FREQUENCY OF ABOUT 35%.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG-3350, ammonium dibasic citrate, potassium phosphate, NaCl, glycerol, beta-mercaptoethanol, alpha-naphthoflavone, CHAPS, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2009 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.7→65.5 Å / Num. all: 15741 / Num. obs: 15741 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 55.387 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 5.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2267 / Rsym value: 0.438 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
CNS1.21refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→65.5 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 781 5 %RANDOM
Rwork0.235 ---
all0.236 15654 --
obs0.236 15654 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.99 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 104.07 Å2 / Biso min: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1--17.145 Å20 Å20 Å2
2--27.701 Å20 Å2
3----10.557 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→65.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 64 33 3752
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONRMSD bond lengths0.011.5
X-RAY DIFFRACTIONRMSD bond angles1.52
X-RAY DIFFRACTIONRMSD dihedral angles22.42
X-RAY DIFFRACTIONRMSD improper angles1.042.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.06
RfactorNum. reflection% reflection
Rfree0.3274 82 -
Rwork0.3187 --
obs-1463 94.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2xdict_heme_relax.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4bhf.par

+
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