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- PDB-3b98: Crystal structure of zebrafish prostacyclin synthase (cytochrome ... -

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Basic information

Entry
Database: PDB / ID: 3b98
TitleCrystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1)
ComponentsProstaglandin I2 synthase
KeywordsISOMERASE / prostacyclin synthase / cytochrome p450 8A1 / CYP8A1
Function / homology
Function and homology information


Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nicotinamide salvaging / Eicosanoids / Sterols are 12-hydroxylated by CYP8B1 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-I synthase / prostaglandin-I synthase activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / hydroperoxy icosatetraenoate dehydratase ...Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nicotinamide salvaging / Eicosanoids / Sterols are 12-hydroxylated by CYP8B1 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-I synthase / prostaglandin-I synthase activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / prostaglandin biosynthetic process / monooxygenase activity / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Prostacyclin synthase / Prostacyclin synthase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLi, Y.-C. / Chiang, C.-W. / Yeh, H.-C. / Hsu, P.-Y. / Whitby, F.G. / Wang, L.-H. / Chan, N.-L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of Prostacyclin Synthase and Its Complexes with Substrate Analog and Inhibitor Reveal a Ligand-specific Heme Conformation Change
Authors: Li, Y.-C. / Chiang, C.-W. / Yeh, H.-C. / Hsu, P.-Y. / Whitby, F.G. / Wang, L.-H. / Chan, N.-L.
History
DepositionNov 3, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_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 / _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: Prostaglandin I2 synthase
B: Prostaglandin I2 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9314
Polymers109,6982
Non-polymers1,2332
Water5,080282
1
A: Prostaglandin I2 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4652
Polymers54,8491
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prostaglandin I2 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4652
Polymers54,8491
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.667, 87.896, 190.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prostaglandin I2 synthase / cytochrome P450 8A1 / prostacyclin synthase


Mass: 54848.930 Da / Num. of mol.: 2 / Fragment: UNP residues 17-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pgis / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: A9LLA5, UniProt: F1RE08*PLUS, prostaglandin-I synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 microliter of concentrated protein solution (20mg/ml) in gel filtration buffer (20mM Tris-HCl pH 8.0, 150mM NaCl and 5mM beta-mercaptoethanol) was mixed with equal amount of reservoir ...Details: 1 microliter of concentrated protein solution (20mg/ml) in gel filtration buffer (20mM Tris-HCl pH 8.0, 150mM NaCl and 5mM beta-mercaptoethanol) was mixed with equal amount of reservoir solution (20% PEG 3350 plus either 50mM Tris-HCl (pH 8.0) or 50mM HEPES (Na-salt; pH 7.5)) and equilibrated against 450 microliter of reservoir solution at 277 K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2006 / Details: Toroidal FM
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. all: 60147 / Num. obs: 60087 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rsym value: 0.046 / Net I/σ(I): 18
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 5912 / Rsym value: 0.21 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IAG

2iag


Resolution: 2.08→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.904 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.254 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26414 3031 5.1 %RANDOM
Rwork0.22735 ---
all0.22921 60147 --
obs0.229 56980 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.442 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7075 0 86 282 7443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227334
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9969934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33323.314350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.895151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4951564
X-RAY DIFFRACTIONr_chiral_restr0.0730.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025562
X-RAY DIFFRACTIONr_nbd_refined0.1860.23379
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2386
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.256
X-RAY DIFFRACTIONr_mcbond_it1.53324509
X-RAY DIFFRACTIONr_mcangle_it2.37537012
X-RAY DIFFRACTIONr_scbond_it1.6923260
X-RAY DIFFRACTIONr_scangle_it2.4832918
LS refinement shellResolution: 2.081→2.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 221 -
Rwork0.224 4091 -
obs-5912 99.1 %

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