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- PDB-1prh: THE X-RAY CRYSTAL STRUCTURE OF THE MEMBRANE PROTEIN PROSTAGLANDIN... -

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Basic information

Entry
Database: PDB / ID: 1prh
TitleTHE X-RAY CRYSTAL STRUCTURE OF THE MEMBRANE PROTEIN PROSTAGLANDIN H2 SYNTHASE-1
ComponentsPROSTAGLANDIN H2 SYNTHASE-1
KeywordsOXIDOREDUCTASE(DIOXYGENASE / PEROXIDASE)
Function / homology
Function and homology information


prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / response to oxidative stress / neuron projection / intracellular membrane-bounded organelle ...prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / prostaglandin biosynthetic process / regulation of blood pressure / peroxidase activity / 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 / Haem peroxidase superfamily ...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 / Prostaglandin G/H synthase 1
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsPicot, D. / Loll, P.J. / Garavito, R.M.
Citation
Journal: Nature / Year: 1994
Title: The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1.
Authors: Picot, D. / Loll, P.J. / Garavito, R.M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: X-Ray Crystal Structure of Canine Myeloperoxidase at 3 Angstroms Resolution
Authors: Zeng, J. / Fenna, R.E.
History
DepositionMar 7, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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
Remark 650HELIX HELIX -- THE NOMENCLATURE FOR THE HELICES 1 - 19 IS BASED ON THE TOPOLOGICAL AND SPATIAL ...HELIX HELIX -- THE NOMENCLATURE FOR THE HELICES 1 - 19 IS BASED ON THE TOPOLOGICAL AND SPATIAL EQUIVALENCE OF SECONDARY STRUCTURE BETWEEN PROSTAGLANDIN H SYNTHASE AND MYELO-PEROXIDASE (ZENG AND FENNA, 1992). HELICES IDENTIFIED WITH A LETTER A - E HAVE NO EQUIVALENT IN MYELOPEROXIDASE.
Remark 700SHEET SHEET -- ONLY A SMALL REGION OF BETA-SHEET IS OBSERVED IN THE EGF-LIKE MODULE (RESIDUES 33 - ...SHEET SHEET -- ONLY A SMALL REGION OF BETA-SHEET IS OBSERVED IN THE EGF-LIKE MODULE (RESIDUES 33 - 72) ALTHOUGH THE EXACT HYDROGEN BONDING SCHEME IS NOT UNEQUIVOCAL AT THE PRESENT RESOLUTION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROSTAGLANDIN H2 SYNTHASE-1
B: PROSTAGLANDIN H2 SYNTHASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9684
Polymers127,7352
Non-polymers1,2332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-66 kcal/mol
Surface area41010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.400, 210.300, 233.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO A 127
2: ASP A 584 - PRO A 585 OMEGA = 240.54 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO B 127
4: ASP B 584 - PRO B 585 OMEGA = 240.42 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99534, -0.0599, 0.07562), (-0.05926, -0.23888, -0.96924), (0.07612, -0.9692, 0.23422)
Vector: 81.43, 234.505, 179.08299)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein PROSTAGLANDIN H2 SYNTHASE-1


Mass: 63867.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep)
References: UniProt: P05979, prostaglandin-endoperoxide synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Compound detailsRESIDUES ASN 68, ASN 144 AND ASN 410 ARE GLYCOSYLATED AND THE FIRST 1 - 2 SUGARS ARE VISIBLE IN THE MAP(S).
Nonpolymer detailsCOX -- THE CYCLOOXYGENASE ACTIVE SITE IS LOCATED WITHIN A LONG HYDROPHOBIC CHANNEL AT A REGION ...COX -- THE CYCLOOXYGENASE ACTIVE SITE IS LOCATED WITHIN A LONG HYDROPHOBIC CHANNEL AT A REGION DEFINED BY RESIDUES ARG 120, SER 530 (SITE OF ASPIRIN ACETYLATION), TYR 385, AND GLU 524. THE CRYSTALS CONTAIN A NON-STEROIDAL ANTI-INFLAMMATORY DRUG FLURBIPROFEN AND THE DRUG BINDING SITE HAS BEEN IDENTIFIED (SEE D. PICOT, P.J. LOLL AND R.M. GARAVITO, 1994), ALTHOUGH REGULARIZED AND REFINED COORDINATES FOR THE PROTEIN-BOUND DRUG ARE NOT YET AVAILABLE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.77 Å3/Da / Density % sol: 74.19 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mMsodium phosphate1drop
2100-200 mM1dropNaCl
30.6 %(w/v)beta-octyl glucopyranoside1drop
40.1 mMflurbiprofen1drop
52-4 %PEG40001drop
620 mMsodium phosphate1reservoir2-4 times concentrate
7100-200 mM1reservoirNaCl2-4 times concentrate
80.6 %(w/v)beta-octyl glucopyranoside1reservoir2-4 times concentrate
90.1 mMflurbiprofen1reservoir2-4 times concentrate
104-8 %PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.4 Å / Num. obs: 32349 / % possible obs: 96.3 % / Num. measured all: 112745 / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→20 Å / σ(F): 2
Details: COORDINATES GIVEN HERE FOR RESIDUES 33 - 586 WHERE THE MAIN CHAIN ELECTRON DENSITY IS WELL DEFINED. ELECTRON DENSITY FOR THE EXTREME AMINO-TERMINUS (RESIDUES 25 - 33) AND THE EXTREME C- ...Details: COORDINATES GIVEN HERE FOR RESIDUES 33 - 586 WHERE THE MAIN CHAIN ELECTRON DENSITY IS WELL DEFINED. ELECTRON DENSITY FOR THE EXTREME AMINO-TERMINUS (RESIDUES 25 - 33) AND THE EXTREME C-TERMINUS (RESIDUES 587 - 600) IS POORLY DEFINED. RESOLUTION IS TOO LIMITED TO CLEARLY DEFINE TURN STEREOCHEMISTRY. PHASED BY MIR (3 DERIVATIVES), SOLVENT FLATTENED AND TWO-FOLD AVERAGED ABOUT THE NON-CRYSTALLOGRAPHIC SYMMETRY AXIS.
RfactorNum. reflection
Rfree0.316 -
Rwork0.267 -
obs0.267 32349
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9006 0 86 0 9092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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