HEADER LIPID TRANSPORT 15-JUL-21 7FCR TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF MUTANTS OF HUMAN TITLE 2 APOLIPOPROTEIN-E (APOE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APO-E; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A+ KEYWDS APOLIPOPROTEIN, LIPID BINDING, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.CHERAKARA,A.KUMAR,K.GARAI,B.GHOSH REVDAT 2 29-NOV-23 7FCR 1 REMARK REVDAT 1 20-JUL-22 7FCR 0 JRNL AUTH S.CHERAKARA,A.KUMAR,K.GARAI,B.GHOSH JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF MUTANTS OF JRNL TITL 2 HUMAN APOLIPOPROTEIN-E (APOE) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 37268 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1829 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 25.8200 - 3.2900 0.99 2928 136 0.1869 0.1901 REMARK 3 2 3.2900 - 2.6100 1.00 2802 147 0.1875 0.1925 REMARK 3 3 2.6100 - 2.2800 1.00 2769 139 0.1555 0.1908 REMARK 3 4 2.2800 - 2.0700 1.00 2745 141 0.1547 0.1919 REMARK 3 5 2.0700 - 1.9200 1.00 2722 145 0.1612 0.1996 REMARK 3 6 1.9200 - 1.8100 1.00 2723 144 0.1500 0.2032 REMARK 3 7 1.8100 - 1.7200 1.00 2723 120 0.1454 0.2048 REMARK 3 8 1.7200 - 1.6500 1.00 2678 157 0.1457 0.1895 REMARK 3 9 1.6500 - 1.5800 0.99 2686 141 0.1399 0.1822 REMARK 3 10 1.5800 - 1.5300 0.99 2684 133 0.1357 0.1662 REMARK 3 11 1.5300 - 1.4800 0.99 2675 145 0.1407 0.1992 REMARK 3 12 1.4800 - 1.4400 0.99 2651 143 0.1797 0.2178 REMARK 3 13 1.4400 - 1.4000 0.99 2653 138 0.2350 0.2830 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.69 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7FCR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.15 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37333 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.94000 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: 1GS9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE, 28% PEG 400, REMARK 280 PH 5.15, MICROBATCH, TEMPERATURE 294K 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 20.32100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.99100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.60350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.99100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.32100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.60350 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 -1 REMARK 465 PRO 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 PRO A 84 REMARK 465 VAL A 85 REMARK 465 ALA A 86 REMARK 465 GLU A 87 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 75 CE NZ REMARK 470 GLN A 81 CD OE1 NE2 REMARK 470 GLU A 88 CD OE1 OE2 REMARK 470 ARG A 90 CZ NH1 NH2 REMARK 470 ARG A 136 NE CZ NH1 NH2 REMARK 470 LYS A 146 NZ REMARK 470 LYS A 157 NZ REMARK 470 GLN A 163 CD OE1 NE2 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 434 DISTANCE = 6.04 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 35 OD1 REMARK 620 2 GLN A 48 OE1 103.4 REMARK 620 3 HOH A 361 O 101.6 52.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 129 O REMARK 620 2 HOH A 414 O 120.5 REMARK 620 N 1 DBREF 7FCR A 1 191 UNP P02649 APOE_HUMAN 19 209 SEQADV 7FCR GLY A -1 UNP P02649 EXPRESSION TAG SEQADV 7FCR PRO A 0 UNP P02649 EXPRESSION TAG SEQADV 7FCR ILE A 112 UNP P02649 CYS 130 ENGINEERED MUTATION SEQRES 1 A 193 GLY PRO LYS VAL GLU GLN ALA VAL GLU THR GLU PRO GLU SEQRES 2 A 193 PRO GLU LEU ARG GLN GLN THR GLU TRP GLN SER GLY GLN SEQRES 3 A 193 ARG TRP GLU LEU ALA LEU GLY ARG PHE TRP ASP TYR LEU SEQRES 4 A 193 ARG TRP VAL GLN THR LEU SER GLU GLN VAL GLN GLU GLU SEQRES 5 A 193 LEU LEU SER SER GLN VAL THR GLN GLU LEU ARG ALA LEU SEQRES 6 A 193 MET ASP GLU THR MET LYS GLU LEU LYS ALA TYR LYS SER SEQRES 7 A 193 GLU LEU GLU GLU GLN LEU THR PRO VAL ALA GLU GLU THR SEQRES 8 A 193 ARG ALA ARG LEU SER LYS GLU LEU GLN ALA ALA GLN ALA SEQRES 9 A 193 ARG LEU GLY ALA ASP MET GLU ASP VAL ILE GLY ARG LEU SEQRES 10 A 193 VAL GLN TYR ARG GLY GLU VAL GLN ALA MET LEU GLY GLN SEQRES 11 A 193 SER THR GLU GLU LEU ARG VAL ARG LEU ALA SER HIS LEU SEQRES 12 A 193 ARG LYS LEU ARG LYS ARG LEU LEU ARG ASP ALA ASP ASP SEQRES 13 A 193 LEU GLN LYS ARG LEU ALA VAL TYR GLN ALA GLY ALA ARG SEQRES 14 A 193 GLU GLY ALA GLU ARG GLY LEU SER ALA ILE ARG GLU ARG SEQRES 15 A 193 LEU GLY PRO LEU VAL GLU GLN GLY ARG VAL ARG HET NA A 201 1 HET NA A 202 1 HETNAM NA SODIUM ION FORMUL 2 NA 2(NA 1+) FORMUL 4 HOH *134(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 80 LEU A 82 5 3 HELIX 5 AA5 THR A 89 MET A 125 1 37 HELIX 6 AA6 THR A 130 GLN A 163 1 34 LINK OD1 ASP A 35 NA NA A 201 1555 1555 2.65 LINK OE1 GLN A 48 NA NA A 201 1555 4557 2.81 LINK O SER A 129 NA NA A 202 1555 1555 2.86 LINK NA NA A 201 O HOH A 361 1555 4457 2.72 LINK NA NA A 202 O HOH A 414 1555 1555 2.77 CRYST1 40.642 53.207 85.982 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 0.024605 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011630 0.00000