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- PDB-2iag: Crystal structure of human prostacyclin synthase -

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Basic information

Entry
Database: PDB / ID: 2iag
TitleCrystal structure of human prostacyclin synthase
ComponentsProstacyclin synthase
KeywordsISOMERASE / prostacyclin synthase / Class III cytochorme P450 / hemoprotein / CYP8A1
Function / homology
Function and homology information


prostaglandin-I synthase / prostaglandin-I synthase activity / Eicosanoids / icosanoid metabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / positive regulation of peroxisome proliferator activated receptor signaling pathway / prostanoid biosynthetic process / : / negative regulation of nitric oxide biosynthetic process ...prostaglandin-I synthase / prostaglandin-I synthase activity / Eicosanoids / icosanoid metabolic process / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / positive regulation of peroxisome proliferator activated receptor signaling pathway / prostanoid biosynthetic process / : / negative regulation of nitric oxide biosynthetic process / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Nicotinamide salvage / cellular response to interleukin-6 / prostaglandin biosynthetic process / negative regulation of NF-kappaB transcription factor activity / positive regulation of execution phase of apoptosis / cellular response to interleukin-1 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / apoptotic signaling pathway / monooxygenase activity / caveola / negative regulation of inflammatory response / positive regulation of angiogenesis / cellular response to hypoxia / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / nucleus
Similarity search - Function
Prostacyclin synthase / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsChiang, C.-W. / Yeh, H.-C. / Wang, L.-H. / Chan, N.-L.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the Human Prostacyclin Synthase
Authors: Chiang, C.-W. / Yeh, H.-C. / Wang, L.-H. / Chan, N.-L.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Prostacyclin synthase
B: Prostacyclin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9675
Polymers110,7112
Non-polymers1,2563
Water7,837435
1
A: Prostacyclin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9722
Polymers55,3551
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prostacyclin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9953
Polymers55,3551
Non-polymers6392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.733, 105.596, 73.950
Angle α, β, γ (deg.)90.00, 92.01, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThere are two prostacyclin synthase molecules in the asymmetric unit, but the enzyme should function as a monomer.

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Components

#1: Protein Prostacyclin synthase / Prostaglandin I2 synthase


Mass: 55355.395 Da / Num. of mol.: 2 / Fragment: residues 23-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Plasmid pCW was a gift from Dr. Amy Roth, University of Oregon.
Gene: PTGIS / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), B834(DE3) / References: UniProt: Q16647, 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: The native recombinant PGIS (25 mg/ml in the buffer containing 20 mM Tris, pH 8.0 and 150 mM NaCl) was found to crystallize spontaneously into needle clusters in the Eppendorf tube when ...Details: The native recombinant PGIS (25 mg/ml in the buffer containing 20 mM Tris, pH 8.0 and 150 mM NaCl) was found to crystallize spontaneously into needle clusters in the Eppendorf tube when stored at 4 C for about a week. A combination of microseeding technique and the hanging-drop vapor-diffusion method was then used to improve crystal quality. Specifically, seed stock was prepared by crushing these initial PGIS needle clusters with the Seed Bead Kit (Hampton Research). Following four 10-fold serial dilutions of the seed stock using the gel filtration buffer, 1 micro-l of diluted seeds was added into a 10 micro-l drop of freshly concentrated PGIS sample, and equilibrated at 4 C against 450 micro-l of the gel filtration buffer. High quality single crystals of PGIS were most often obtained using 100- or 1000-fold diluted seed stock, and reached suitable size (~ 0.05,0.05 ~ 0.1 mm3) within one week., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B110.980127
SYNCHROTRONSPring-8 BL12B220.9537, 0.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 29, 2006
ADSC QUANTUM 42CCDMay 15, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9801271
20.95371
30.97931
ReflectionResolution: 2.15→30 Å / Num. all: 56459 / Num. obs: 51322 / % possible obs: 90.9 % / Redundancy: 2.8 % / Rsym value: 0.063 / Net I/σ(I): 12.7
Reflection shellResolution: 2.15→2.23 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.35 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→20.15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.798 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26313 2601 5.1 %RANDOM
Rwork0.2009 ---
obs0.20407 48702 90.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.948 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7611 0 87 435 8133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227915
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.382.00110757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25622.433374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.588151325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4331574
X-RAY DIFFRACTIONr_chiral_restr0.0950.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026066
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23657
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25280
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2480
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.54689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21327541
X-RAY DIFFRACTIONr_scbond_it1.96133373
X-RAY DIFFRACTIONr_scangle_it2.9874.53216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 195 -
Rwork0.215 3616 -
obs--93.29 %

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