PDB Short entry for 1NFN HEADER LIPID TRANSPORT 17-JUL-96 1NFN TITLE APOLIPOPROTEIN E3 (APOE3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN E3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 22KD RECEPTOR BINDING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: PLASMA; SOURCE 6 GENE: E2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID TRANSPORT, HEPARIN-BINDING, PLASMA PROTEIN, HDL, VLDL EXPDTA X-RAY DIFFRACTION AUTHOR B.RUPP,S.PARKIN REVDAT 4 09-AUG-23 1NFN 1 REMARK REVDAT 3 24-FEB-09 1NFN 1 VERSN REVDAT 2 01-APR-03 1NFN 1 JRNL REVDAT 1 27-JAN-97 1NFN 0 JRNL AUTH L.M.DONG,S.PARKIN,S.D.TRAKHANOV,B.RUPP,T.SIMMONS,K.S.ARNOLD, JRNL AUTH 2 Y.M.NEWHOUSE,T.L.INNERARITY,K.H.WEISGRABER JRNL TITL NOVEL MECHANISM FOR DEFECTIVE RECEPTOR BINDING OF JRNL TITL 2 APOLIPOPROTEIN E2 IN TYPE III HYPERLIPOPROTEINEMIA. JRNL REF NAT.STRUCT.BIOL. V. 3 718 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8756331 JRNL DOI 10.1038/NSB0896-718 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-93 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 CROSS-VALIDATION METHOD : R-FREE REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 10TH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.213 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.209 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1656 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 16562 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.209 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1088 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5787 REMARK 3 NUMBER OF RESTRAINTS : 5176 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 2.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.110 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.064 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.072 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.054 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: 'SWAT' IN SHELXL93 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175269. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : ADSC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.03730 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT WITH REMARK 200 PHASE IMPROVEMENT BY HOLOGRAPHIC RECONSTRUCTION OF ELECTRON REMARK 200 DENSITY REMARK 200 SOFTWARE USED: SHELXL-93, X-PLOR REMARK 200 STARTING MODEL: PHASING MODEL DERIVED FROM PDB ENTRY 1LPE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 20.35050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.25450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.67750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.25450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.35050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.67750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 1 REMARK 465 VAL A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 ALA A 5 REMARK 465 VAL A 6 REMARK 465 GLU A 7 REMARK 465 THR A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 GLU A 11 REMARK 465 PRO A 12 REMARK 465 GLU A 13 REMARK 465 LEU A 14 REMARK 465 ARG A 15 REMARK 465 GLN A 16 REMARK 465 GLN A 17 REMARK 465 THR A 18 REMARK 465 GLU A 19 REMARK 465 TRP A 20 REMARK 465 GLN A 21 REMARK 465 SER A 22 REMARK 465 LEU A 82 REMARK 465 THR A 83 REMARK 465 PRO A 84 REMARK 465 VAL A 85 REMARK 465 ALA A 86 REMARK 465 GLU A 87 REMARK 465 GLU A 88 REMARK 465 THR A 89 REMARK 465 ARG A 90 REMARK 465 ALA A 91 REMARK 465 GLY A 165 REMARK 465 ALA A 166 REMARK 465 ARG A 167 REMARK 465 GLU A 168 REMARK 465 GLY A 169 REMARK 465 ALA A 170 REMARK 465 GLU A 171 REMARK 465 ARG A 172 REMARK 465 GLY A 173 REMARK 465 LEU A 174 REMARK 465 SER A 175 REMARK 465 ALA A 176 REMARK 465 ILE A 177 REMARK 465 ARG A 178 REMARK 465 GLU A 179 REMARK 465 ARG A 180 REMARK 465 LEU A 181 REMARK 465 GLY A 182 REMARK 465 PRO A 183 REMARK 465 LEU A 184 REMARK 465 VAL A 185 REMARK 465 GLU A 186 REMARK 465 GLN A 187 REMARK 465 GLY A 188 REMARK 465 ARG A 189 REMARK 465 VAL A 190 REMARK 465 ARG A 191 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 32 OE2 GLU A 66 1.84 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 145 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES 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 GLN A 24 124.90 156.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 61 0.22 SIDE CHAIN REMARK 500 ARG A 92 0.09 SIDE CHAIN REMARK 500 ARG A 103 0.13 SIDE CHAIN REMARK 500 ARG A 119 0.15 SIDE CHAIN REMARK 500 ARG A 134 0.26 SIDE CHAIN REMARK 500 ARG A 136 0.24 SIDE CHAIN REMARK 500 ARG A 145 0.08 SIDE CHAIN REMARK 500 ARG A 147 0.13 SIDE CHAIN REMARK 500 ARG A 158 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1NFN A 1 191 UNP P02649 APOE_HUMAN 19 209 SEQRES 1 A 191 LYS VAL GLU GLN ALA VAL GLU THR GLU PRO GLU PRO GLU SEQRES 2 A 191 LEU ARG GLN GLN THR GLU TRP GLN SER GLY GLN ARG TRP SEQRES 3 A 191 GLU LEU ALA LEU GLY ARG PHE TRP ASP TYR LEU ARG TRP SEQRES 4 A 191 VAL GLN THR LEU SER GLU GLN VAL GLN GLU GLU LEU LEU SEQRES 5 A 191 SER SER GLN VAL THR GLN GLU LEU ARG ALA LEU MET ASP SEQRES 6 A 191 GLU THR MET LYS GLU LEU LYS ALA TYR LYS SER GLU LEU SEQRES 7 A 191 GLU GLU GLN LEU THR PRO VAL ALA GLU GLU THR ARG ALA SEQRES 8 A 191 ARG LEU SER LYS GLU LEU GLN ALA ALA GLN ALA ARG LEU SEQRES 9 A 191 GLY ALA ASP MET GLU ASP VAL CYS GLY ARG LEU VAL GLN SEQRES 10 A 191 TYR ARG GLY GLU VAL GLN ALA MET LEU GLY GLN SER THR SEQRES 11 A 191 GLU GLU LEU ARG VAL ARG LEU ALA SER HIS LEU ARG LYS SEQRES 12 A 191 LEU ARG LYS ARG LEU LEU ARG ASP ALA ASP ASP LEU GLN SEQRES 13 A 191 LYS ARG LEU ALA VAL TYR GLN ALA GLY ALA ARG GLU GLY SEQRES 14 A 191 ALA GLU ARG GLY LEU SER ALA ILE ARG GLU ARG LEU GLY SEQRES 15 A 191 PRO LEU VAL GLU GLN GLY ARG VAL ARG FORMUL 2 HOH *155(H2 O) HELIX 1 1 ARG A 25 THR A 42 1 18 HELIX 2 2 GLU A 45 LEU A 52 1 8 HELIX 3 3 GLN A 55 GLU A 80 1 26 HELIX 4 4 LEU A 93 MET A 125 1 33 HELIX 5 5 GLU A 131 TYR A 162 1 32 CRYST1 40.701 53.355 84.509 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.024569 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011833 0.00000