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- PDB-3pm0: Structural Characterization of the Complex between Alpha-Naphthof... -

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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


cellular response to cortisol stimulus / response to indole-3-methanol / Defective CYP1B1 causes Glaucoma / trabecular meshwork development / benzene-containing compound metabolic process / endothelial cell-cell adhesion / membrane lipid catabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / ganglion development ...cellular response to cortisol stimulus / response to indole-3-methanol / Defective CYP1B1 causes Glaucoma / trabecular meshwork development / benzene-containing compound metabolic process / endothelial cell-cell adhesion / membrane lipid catabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / ganglion development / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / response to follicle-stimulating hormone / retinal blood vessel morphogenesis / omega-hydroxylase P450 pathway / response to 3-methylcholanthrene / toxin metabolic process / arachidonate metabolic process / epoxygenase P450 pathway / blood vessel endothelial cell migration / estrogen 16-alpha-hydroxylase activity / DNA modification / retinal metabolic process / cellular response to progesterone stimulus / sterol metabolic process / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / cellular response to luteinizing hormone stimulus / negative regulation of cell adhesion mediated by integrin / cellular response to toxic substance / 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 / retinol metabolic process / estrogen metabolic process / regulation of reactive oxygen species metabolic process / unspecific monooxygenase / aromatase activity / intrinsic apoptotic signaling pathway in response to oxidative stress / adrenal gland development / negative regulation of NF-kappaB transcription factor activity / positive regulation of DNA biosynthetic process / positive regulation of smooth muscle cell migration / response to dexamethasone / steroid metabolic process / cellular response to organic cyclic compound / positive regulation of vascular endothelial growth factor production / endothelial cell migration / estrous cycle / Endogenous sterols / cellular response to cAMP / nitric oxide biosynthetic process / xenobiotic metabolic process / response to nutrient / negative regulation of cell migration / positive regulation of translation / monooxygenase activity / 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 / cellular response to tumor necrosis factor / response to estradiol / angiogenesis / cell adhesion / positive regulation of apoptotic process / iron ion binding / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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%.

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Experimental details

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Experiment

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

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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

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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

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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

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