HEADER LIPID TRANSPORT 21-JAN-99 1B68 TITLE APOLIPOPROTEIN E4 (APOE4), 22K FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 22K FRAGMENT, ISOFORM E4, RECEPTOR BINDING DOMAIN, RESIDUES COMPND 5 1-191; COMPND 6 SYNONYM: APOE4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS LIPID TRANSPORT, HEPARIN-BINDING, PLASMA PROTEIN, HDL, VLDL EXPDTA X-RAY DIFFRACTION AUTHOR B.RUPP,C.PETERS-LIBEU REVDAT 4 09-AUG-23 1B68 1 REMARK REVDAT 3 24-FEB-09 1B68 1 VERSN REVDAT 2 01-APR-03 1B68 1 JRNL REVDAT 1 11-JUL-01 1B68 0 JRNL AUTH J.DONG,C.A.PETERS-LIBEU,K.H.WEISGRABER,B.W.SEGELKE,B.RUPP, JRNL AUTH 2 I.CAPILA,M.J.HERNAIZ,L.A.LEBRUN,R.J.LINHARDT JRNL TITL INTERACTION OF THE N-TERMINAL DOMAIN OF APOLIPOPROTEIN E4 JRNL TITL 2 WITH HEPARIN. JRNL REF BIOCHEMISTRY V. 40 2826 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11258893 JRNL DOI 10.1021/BI002417N REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 11931 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1197 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1650 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 183 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1140 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : 0.68000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.24 REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.510 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1B68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-99. REMARK 100 THE DEPOSITION ID IS D_1000001543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 125.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16493 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 27.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : 0.19900 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR, CCP4 REMARK 200 STARTING MODEL: 1BZ4 REMARK 200 REMARK 200 REMARK: RIGID BODY REFINEMENT ONLY, THEN REBUILD, WARP MAPS USED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL : 28% PEG 400, 20MM NAOAC, PH REMARK 280 6.0, 0.1% BME PROTEIN SOLN: 40MM (NH4)H(CO3), 7MG/ML PROTEIN REMARK 280 DROPS : WELL/PROTEIN 1/3, ROOM TEMPERATURE, PH 6.00, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 20.10500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.38000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.60500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.38000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.10500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.60500 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 PRO A 84 REMARK 465 VAL A 85 REMARK 465 GLN A 163 REMARK 465 ALA A 164 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: 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 81 53.10 -142.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 1B68 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 ARG 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 *133(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 GLU A 87 ALA A 124 1 38 HELIX 5 5 GLU A 131 ALA A 160 1 30 CRYST1 40.210 53.210 84.760 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 0.024869 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011798 0.00000