HEADER LIPID TRANSPORT 07-AUG-25 9SA6 TITLE HUMAN APOLIPOPROTEIN E4 (APOE4) N-TERMINAL DOMAIN (SPACE GROUP TITLE 2 P212121) COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APO-E; 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 GENE: APOE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS APOLIPOPROTEIN E, CHOLESTEROL BINDING AND TRANSPORT, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.MAREK,K.SNAJDAROVA REVDAT 1 19-AUG-26 9SA6 0 JRNL AUTH M.MAREK,K.SNAJDAROVA JRNL TITL HUMAN APOLIPOPROTEIN E4 (APOE4) N-TERMINAL DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14514 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 706 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.4940 - 3.2365 1.00 2902 144 0.1682 0.2038 REMARK 3 2 3.2365 - 2.5691 1.00 2758 155 0.1882 0.2395 REMARK 3 3 2.5691 - 2.2444 1.00 2745 140 0.1800 0.2295 REMARK 3 4 2.2444 - 2.0392 1.00 2727 131 0.1902 0.2691 REMARK 3 5 2.0392 - 1.8930 0.99 2676 136 0.2503 0.3198 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.015 1242 REMARK 3 ANGLE : 1.261 1665 REMARK 3 CHIRALITY : 0.075 179 REMARK 3 PLANARITY : 0.007 218 REMARK 3 DIHEDRAL : 11.245 1072 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 17.5012 41.8364 49.7196 REMARK 3 T TENSOR REMARK 3 T11: 0.2097 T22: 0.2125 REMARK 3 T33: 0.2010 T12: -0.0023 REMARK 3 T13: -0.0224 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.3225 L22: 0.6584 REMARK 3 L33: 0.1749 L12: -0.3783 REMARK 3 L13: 0.1598 L23: -0.0550 REMARK 3 S TENSOR REMARK 3 S11: -0.0657 S12: 0.0131 S13: -0.0382 REMARK 3 S21: 0.1297 S22: 0.0179 S23: -0.0555 REMARK 3 S31: -0.0498 S32: 0.0009 S33: -0.0029 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9SA6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1292150048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.967697 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14563 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 45.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM FORMATE, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 22.63100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.58850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.46550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.58850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.63100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.46550 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 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 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 465 ALA A 192 REMARK 465 ALA A 193 REMARK 465 THR A 194 REMARK 465 VAL A 195 REMARK 465 GLY A 196 REMARK 465 SER A 197 REMARK 465 LEU A 198 REMARK 465 ALA A 199 REMARK 465 GLY A 200 REMARK 465 GLN A 201 REMARK 465 PRO A 202 REMARK 465 LEU A 203 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 38 NE - CZ - NH1 ANGL. DEV. = -3.8 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 81 53.42 -142.86 REMARK 500 ALA A 86 18.14 -53.25 REMARK 500 GLU A 87 -57.74 61.91 REMARK 500 LEU A 126 -132.54 52.68 REMARK 500 GLN A 163 -70.85 -44.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 492 DISTANCE = 7.80 ANGSTROMS REMARK 525 HOH A 493 DISTANCE = 9.88 ANGSTROMS DBREF 9SA6 A 1 203 UNP P02649 APOE_HUMAN 19 221 SEQADV 9SA6 GLY A -3 UNP P02649 EXPRESSION TAG SEQADV 9SA6 PRO A -2 UNP P02649 EXPRESSION TAG SEQADV 9SA6 HIS A -1 UNP P02649 EXPRESSION TAG SEQADV 9SA6 MET A 0 UNP P02649 EXPRESSION TAG SEQADV 9SA6 ARG A 112 UNP P02649 CYS 130 CONFLICT SEQRES 1 A 207 GLY PRO HIS MET LYS VAL GLU GLN ALA VAL GLU THR GLU SEQRES 2 A 207 PRO GLU PRO GLU LEU ARG GLN GLN THR GLU TRP GLN SER SEQRES 3 A 207 GLY GLN ARG TRP GLU LEU ALA LEU GLY ARG PHE TRP ASP SEQRES 4 A 207 TYR LEU ARG TRP VAL GLN THR LEU SER GLU GLN VAL GLN SEQRES 5 A 207 GLU GLU LEU LEU SER SER GLN VAL THR GLN GLU LEU ARG SEQRES 6 A 207 ALA LEU MET ASP GLU THR MET LYS GLU LEU LYS ALA TYR SEQRES 7 A 207 LYS SER GLU LEU GLU GLU GLN LEU THR PRO VAL ALA GLU SEQRES 8 A 207 GLU THR ARG ALA ARG LEU SER LYS GLU LEU GLN ALA ALA SEQRES 9 A 207 GLN ALA ARG LEU GLY ALA ASP MET GLU ASP VAL ARG GLY SEQRES 10 A 207 ARG LEU VAL GLN TYR ARG GLY GLU VAL GLN ALA MET LEU SEQRES 11 A 207 GLY GLN SER THR GLU GLU LEU ARG VAL ARG LEU ALA SER SEQRES 12 A 207 HIS LEU ARG LYS LEU ARG LYS ARG LEU LEU ARG ASP ALA SEQRES 13 A 207 ASP ASP LEU GLN LYS ARG LEU ALA VAL TYR GLN ALA GLY SEQRES 14 A 207 ALA ARG GLU GLY ALA GLU ARG GLY LEU SER ALA ILE ARG SEQRES 15 A 207 GLU ARG LEU GLY PRO LEU VAL GLU GLN GLY ARG VAL ARG SEQRES 16 A 207 ALA ALA THR VAL GLY SER LEU ALA GLY GLN PRO LEU HET GOL A 301 6 HET GOL A 302 6 HET GOL A 303 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *93(H2 O) HELIX 1 AA1 GLN A 24 LEU A 43 1 20 HELIX 2 AA2 SER A 44 SER A 53 1 10 HELIX 3 AA3 SER A 54 GLU A 79 1 26 HELIX 4 AA4 GLU A 87 MET A 125 1 39 HELIX 5 AA5 THR A 130 GLY A 165 1 36 CRYST1 45.262 52.931 73.177 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 0.022094 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013665 0.00000 CONECT 1213 1214 1215 CONECT 1214 1213 CONECT 1215 1213 1216 1217 CONECT 1216 1215 CONECT 1217 1215 1218 CONECT 1218 1217 CONECT 1219 1220 1221 CONECT 1220 1219 CONECT 1221 1219 1222 1223 CONECT 1222 1221 CONECT 1223 1221 1224 CONECT 1224 1223 CONECT 1225 1226 1227 CONECT 1226 1225 CONECT 1227 1225 1228 1229 CONECT 1228 1227 CONECT 1229 1227 1230 CONECT 1230 1229 MASTER 332 0 3 5 0 0 0 6 1283 1 18 16 END