PDB Short entry for 1IOJ HEADER APOLIPOPROTEIN 12-MAY-98 1IOJ TITLE HUMAN APOLIPOPROTEIN C-I, NMR, 18 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOC-I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS APOLIPOPROTEIN, AMPHIPATHIC HELIX, LIPID ASSOCIATION, LCAT ACTIVATION EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR A.ROZEK,J.T.SPARROW,K.H.WEISGRABER,R.J.CUSHLEY REVDAT 3 14-MAR-18 1IOJ 1 COMPND SOURCE REMARK REVDAT 2 24-FEB-09 1IOJ 1 VERSN REVDAT 1 12-AUG-98 1IOJ 0 JRNL AUTH A.ROZEK,J.T.SPARROW,K.H.WEISGRABER,R.J.CUSHLEY JRNL TITL CONFORMATION OF HUMAN APOLIPOPROTEIN C-I IN A LIPID-MIMETIC JRNL TITL 2 ENVIRONMENT DETERMINED BY CD AND NMR SPECTROSCOPY. JRNL REF BIOCHEMISTRY V. 38 14475 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10545169 JRNL DOI 10.1021/BI982966H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DGII, DISCOVER DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC, SAN DIEGO REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE OF APOC-I(1-38) IN THE REMARK 3 PRESENCE OF SODIUM DODECYL SULFATE WAS REFINED USING 685 NOE- REMARK 3 BASED DISTANCE RESTRAINTS. NO DIHEDRAL RESTRAINTS AND NO H-BOND REMARK 3 RESTRAINTS WERE USED. THIS ENTRY CONTAINS 18 ACCEPTED OUT OF 50 REMARK 3 CALCULATED STRUCTURES. STRUCTURE CALCULATIONS WERE PERFORMED REMARK 3 WITH THE PROGRAMS DGII AND DISCOVER INCLUDING DISTANCE GEOMETRY REMARK 3 CALCULATIONS, SIMULATED ANNEALING AND ENERGY MINIMIZATION WITH A REMARK 3 CONJUGATED GRADIENT. THE CVFF FORCEFIELD WAS USED. ALL FORMAL REMARK 3 CHARGES WERE SWITCHED OFF. THE DIELECTRIC CONSTANT WAS SET TO 1. REMARK 3 THE LENNARD-JONES POTENTIAL WAS USED FOR NON-BOND INTERACTIONS REMARK 3 (CUTOFF 12A). FOR DETAILS ON STRUCTURE CALCULATION, RMSDS AND REMARK 3 FINAL ENERGIES PLEASE SEE REFERENCE CITED UNDER "JRNL". REMARK 4 REMARK 4 1IOJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174223. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323 REMARK 210 PH : 4.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 5.8 MM NATIVE APOC-I, REMARK 210 90%H2O/10%D2O, 232 MM SDS-D25; 5 REMARK 210 MM SELECTIVELY 15N-LABELED REMARK 210 SYNTHETIC APOC-I, 90%H2O/10%D2O, REMARK 210 200 MM SDS-D25 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D-NOESY; 2D-TOCSY; DQF-COSY; 2D REMARK 210 -15N-FILTERED NOESY; 2D-15N- REMARK 210 FILTERED TOCSY; 2D 1H-15N HSQC; REMARK 210 3D-NOESY-HSQC; 3D-TOCSY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX 600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DGII AND DISCOVER DISCOVER REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : SELECTED STRUCTURES HAVE NO REMARK 210 HELIX-HELIX CONTACTS <5 ANGSTROMS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 REMARK 210 REMARK 210 REMARK: USING WATERGATE FOR WATER SUPPRESSION, 2D-TOCSY USING MLEV REMARK 210 -17 FOR MIXING, 3D-TOCSY USING DIPSY-2RC FOR MIXING. 15N- REMARK 210 FILTERED NOESY AND TOCSY INCLUDE DIFFERENCE (SHOWING ONLY 15N REMARK 210 LABELED RESIDUES) AND SUM SPECTRA (SHOWING ONLY UNLABELED REMARK 210 RESIDUES). REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 MET A 38 N - CA - CB ANGL. DEV. = -11.5 DEGREES REMARK 500 2 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 GLU A 33 N - CA - CB ANGL. DEV. = 11.1 DEGREES REMARK 500 3 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 MET A 38 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 4 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 8 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 8 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 9 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 10 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 10 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 VAL A 4 CB - CA - C ANGL. DEV. = 11.6 DEGREES REMARK 500 11 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 12 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 12 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 12 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 13 ALA A 36 N - CA - CB ANGL. DEV. = 11.0 DEGREES REMARK 500 13 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 14 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 14 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 GLU A 40 N - CA - CB ANGL. DEV. = 11.0 DEGREES REMARK 500 15 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 61 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 5 73.21 -152.38 REMARK 500 1 ALA A 7 -66.32 -121.58 REMARK 500 1 GLU A 24 -62.76 169.28 REMARK 500 1 ARG A 28 -53.52 141.66 REMARK 500 1 ILE A 29 -81.65 -76.36 REMARK 500 1 SER A 32 -97.41 -117.90 REMARK 500 1 SER A 35 -110.03 -87.03 REMARK 500 1 ALA A 36 -68.92 70.23 REMARK 500 1 GLU A 44 -63.73 175.10 REMARK 500 1 LEU A 53 -128.48 -103.17 REMARK 500 1 LYS A 54 -113.97 59.10 REMARK 500 1 ILE A 55 -67.91 -92.18 REMARK 500 1 ASP A 56 -87.18 -140.65 REMARK 500 2 VAL A 4 -121.72 -128.94 REMARK 500 2 ALA A 7 -56.67 -130.80 REMARK 500 2 LYS A 12 -76.00 70.37 REMARK 500 2 LEU A 18 46.10 -98.72 REMARK 500 2 GLU A 19 52.18 -117.51 REMARK 500 2 ASP A 20 -55.63 -171.27 REMARK 500 2 ARG A 23 -60.35 -122.33 REMARK 500 2 ILE A 29 -70.44 -100.72 REMARK 500 2 LEU A 53 -68.64 -100.29 REMARK 500 2 ILE A 55 89.18 65.33 REMARK 500 3 VAL A 4 -148.00 -100.56 REMARK 500 3 SER A 6 -70.41 -172.90 REMARK 500 3 ALA A 7 -33.45 76.62 REMARK 500 3 ILE A 29 -82.55 -68.05 REMARK 500 3 GLN A 31 74.18 54.14 REMARK 500 3 SER A 32 153.54 71.95 REMARK 500 3 GLU A 33 -42.01 127.44 REMARK 500 3 SER A 35 -110.49 -79.97 REMARK 500 3 ALA A 36 -66.48 71.18 REMARK 500 3 MET A 38 0.61 -68.95 REMARK 500 3 ARG A 39 -63.37 -122.57 REMARK 500 3 GLU A 44 -69.46 171.52 REMARK 500 3 PHE A 46 -64.00 -91.37 REMARK 500 3 LYS A 54 -173.17 55.92 REMARK 500 3 ILE A 55 -79.17 -113.74 REMARK 500 3 ASP A 56 -80.07 -87.83 REMARK 500 4 ASP A 3 146.70 177.22 REMARK 500 4 VAL A 4 -129.93 -114.94 REMARK 500 4 ALA A 7 -44.39 -137.92 REMARK 500 4 LYS A 12 -76.44 68.75 REMARK 500 4 ILE A 29 -93.63 -78.49 REMARK 500 4 LYS A 30 2.87 56.35 REMARK 500 4 GLN A 31 -8.02 -161.23 REMARK 500 4 GLU A 33 -9.07 69.06 REMARK 500 4 SER A 35 105.57 -161.02 REMARK 500 4 LYS A 54 96.98 91.25 REMARK 500 5 ASP A 3 -92.84 71.25 REMARK 500 REMARK 500 THIS ENTRY HAS 198 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 18 GLU A 19 2 137.49 REMARK 500 GLU A 33 LEU A 34 2 149.05 REMARK 500 GLU A 33 LEU A 34 4 141.07 REMARK 500 GLU A 33 LEU A 34 5 144.46 REMARK 500 GLY A 15 ASN A 16 6 141.49 REMARK 500 LEU A 34 SER A 35 6 148.72 REMARK 500 SER A 35 ALA A 36 6 -149.07 REMARK 500 GLU A 33 LEU A 34 7 149.44 REMARK 500 GLU A 33 LEU A 34 11 142.74 REMARK 500 SER A 35 ALA A 36 12 147.59 REMARK 500 GLU A 33 LEU A 34 13 146.65 REMARK 500 SER A 35 ALA A 36 13 -144.54 REMARK 500 GLU A 33 LEU A 34 17 143.35 REMARK 500 SER A 35 ALA A 36 17 138.60 REMARK 500 LEU A 34 SER A 35 18 -127.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IOJ A 1 57 UNP P02654 APOC1_HUMAN 27 83 SEQRES 1 A 57 THR PRO ASP VAL SER SER ALA LEU ASP LYS LEU LYS GLU SEQRES 2 A 57 PHE GLY ASN THR LEU GLU ASP LYS ALA ARG GLU LEU ILE SEQRES 3 A 57 SER ARG ILE LYS GLN SER GLU LEU SER ALA LYS MET ARG SEQRES 4 A 57 GLU TRP PHE SER GLU THR PHE GLN LYS VAL LYS GLU LYS SEQRES 5 A 57 LEU LYS ILE ASP SER HELIX 1 1 LEU A 8 LEU A 11 1 4 HELIX 2 2 PHE A 14 ILE A 29 1 16 HELIX 3 3 LYS A 37 LYS A 50 1 14 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 -1.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000