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- PDB-1ebv: OVINE PGHS-1 COMPLEXED WITH SALICYL HYDROXAMIC ACID -

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Basic information

Entry
Database: PDB / ID: 1ebv
TitleOVINE PGHS-1 COMPLEXED WITH SALICYL HYDROXAMIC ACID
ComponentsPROSTAGLANDIN H2 SYNTHASE
KeywordsOXIDOREDUCTASE / monotopic membrane protein
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin biosynthetic process / peroxidase activity / regulation of blood pressure / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain ...: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / ACETIC ACID SALICYLOYL-AMINO-ESTER / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsLoll, P.J. / Sharkey, C.T. / O'Connor, S.J. / Fitzgerald, D.J.
CitationJournal: Mol.Pharmacol. / Year: 2001
Title: O-acetylsalicylhydroxamic acid, a novel acetylating inhibitor of prostaglandin H2 synthase: structural and functional characterization of enzyme-inhibitor interactions.
Authors: Loll, P.J. / Sharkey, C.T. / O'Connor, S.J. / Dooley, C.M. / O'Brien, E. / Devocelle, M. / Nolan, K.B. / Selinsky, B.S. / Fitzgerald, D.J.
History
DepositionJan 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROSTAGLANDIN H2 SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2326
Polymers63,5541
Non-polymers1,6785
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.870, 207.460, 221.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROSTAGLANDIN H2 SYNTHASE


Mass: 63553.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: SEMINAL VESICLES
References: UniProt: P05979, prostaglandin-endoperoxide synthase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-SCL / ACETIC ACID SALICYLOYL-AMINO-ESTER


Mass: 195.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO4
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has protein modificationY

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG4000, sodium phosphate, octyl glucoside, sodium chloride, diethyldithiocarbamate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16.5 %PEG40001reservoir
265 mMsodium phosphate1reservoirpH6.7
3410 mM1reservoirNaCl
412 mg/mlenzyme1drop
520 mMsodium phosphate1droppH6.7
6100 mM1dropNaCl
70.6 %(w/w)beta-octylglucoside1drop
80.100 mMdiethyldithiocarbamate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→23.5 Å / Num. all: 38087 / Num. obs: 31170 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 13
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.25 / Num. unique all: 4899 / % possible all: 78.3
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 35021 / Num. measured all: 124009
Reflection shell
*PLUS
Lowest resolution: 3.3 Å / % possible obs: 75 % / Rmerge(I) obs: 0.289

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
CNS0.9refinement
X-PLORphasing
RefinementResolution: 3.2→23.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2502 6.6 %Random
Rwork0.218 ---
all0.225 31170 --
obs0.225 31170 81.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.047 Å20 Å20 Å2
2---0.699 Å20 Å2
3----1.348 Å2
Refinement stepCycle: LAST / Resolution: 3.2→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4481 0 113 0 4594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg21.7
X-RAY DIFFRACTIONc_torsion_impr_deg0.9
X-RAY DIFFRACTIONc_mcbond_it0.971
X-RAY DIFFRACTIONc_mcangle_it1.7461.5
X-RAY DIFFRACTIONc_scbond_it1.4171.5
X-RAY DIFFRACTIONc_scangle_it2.3982
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3HEM.PAR
X-RAY DIFFRACTION4ACETYL_SERINE.PARAM
X-RAY DIFFRACTION5SAL.PAR
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 23.5 Å / σ(F): 0 / % reflection Rfree: 6.6 % / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
X-RAY DIFFRACTIONc_mcbond_it1
X-RAY DIFFRACTIONc_scbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it1.5
X-RAY DIFFRACTIONc_scangle_it2

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